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  • 1. Aalto, Juha
    et al.
    Riihimäki, Henri
    Meineri, Eric
    Hylander, Kristoffer
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Luoto, Miska
    Revealing topoclimatic heterogeneity using meteorological station data2017Ingår i: International Journal of Climatology, ISSN 0899-8418, E-ISSN 1097-0088, Vol. 37, nr Suppl. 1, s. 544-556Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Climate is a crucial driver of the distributions and activity of multiple biotic and abiotic processes, and thus high-quality and high-resolution climate data are often prerequisite in various environmental research. However, contemporary gridded climate products suffer critical problems mainly related to sub-optimal pixel size and lack of local topography-driven temperature heterogeneity. Here, by integrating meteorological station data, high-quality terrain information and multivariate modelling, we aim to explicitly demonstrate this deficiency. Monthly average temperatures (1981-2010) from Finland, Sweden and Norway were modelled using generalized additive modelling under (1) a conventional (i.e. considering geographical location, elevation and water cover) and (2) a topoclimatic framework (i.e. also accounting for solar radiation and cold-air pooling). The performance of the topoclimatic model was significantly higher than the conventional approach for most months, with bootstrapped mean R-2 for the topoclimatic model varying from 0.88 (January) to 0.95 (October). The estimated effect of solar radiation was evident during summer, while cold air pooling was identified to improve local temperature estimates in winter. The topoclimatic modelling exposed a substantial temperature heterogeneity within coarser landscape units (>5 degrees C/1 km(-2) in summer) thus unveiling a wide range of potential microclimatic conditions neglected by the conventional approach. Moreover, the topoclimatic model predictions revealed a pronounced asymmetry in average temperature conditions, causing isotherms during summer to differ several hundreds of metres in altitude between the equator and pole facing slopes. In contrast, cold-air pooling in sheltered landscapes lowered the winter temperatures ca. 1.1 degrees C/100m towards the local minimum altitude. Noteworthy, the analysis implies that conventional models produce biassed predictions of long-term average temperature conditions, with errors likely to be high at sites associated with complex topography.

  • 2.
    Abdelfattah, Ahmed
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Graz University of Technology, Austria.
    Freilich, Shiri
    Bartuv, Rotem
    Zhimo, V. Yeka
    Kumar, Ajay
    Biasi, Antonio
    Salim, Shoshana
    Feygenberg, Oleg
    Burchard, Erik
    Dardick, Christopher
    Liu, Jia
    Khan, Awais
    Ellouze, Walid
    Ali, Shawkat
    Spadaro, Davide
    Torres, Rosario
    Teixido, Neus
    Ozkaya, Okan
    Buehlmann, Andreas
    Vero, Silvana
    Mondino, Pedro
    Berg, Gabriele
    Wisniewski, Michael
    Droby, Samir
    Global analysis of the apple fruit microbiome: are all apples the same?2021Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 23, nr 10, s. 6038-6055Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present the first worldwide study on the apple (Malus x domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit vary and are highly dependent on geographical location. The study also confirmed that the spatial variation in the fungal and bacterial composition of different fruit tissues exists at a global level. Fungal diversity varied significantly in fruit harvested in different geographical locations and suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. The study provides foundational information about the apple fruit microbiome that can be utilized for the development of novel approaches for the management of fruit quality and safety, as well as for reducing losses due to the establishment and proliferation of postharvest pathogens. It also lays the groundwork for studying the complex microbial interactions that occur on apple fruit surfaces.

  • 3.
    Abdelfattah, Ahmed
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Università Mediterranea di Reggio Calabria, Italy.
    Ruano-Rosa, David
    Cacciola, Santa Olga
    Nicosia, Maria G. Li Destri
    Schena, Leonardo
    Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes2018Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 13, nr 11, artikel-id e0199403Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The olive fruit fly (OFF), Bactrocera oleae is the most devastating pest affecting olive fruit worldwide. Previous investigations have addressed the fungal microbiome associated with olive drupes or B. oleae, but the impact of the insect on fungal communities of olive fruit remains undescribed. In the present work, the fungal microbiome of olive drupes, infested and non-infested by the OFF, was investigated in four different localities and cultivars. Olive fruit fly infestations caused a general reduction of the fungal diversity, a higher quantity of the total DNA and an increase in taxa that remained unidentified or had unknown roles. The infestations led to imbalanced fungal communities with the growth of taxa that are usually outcompeted. While it was difficult to establish a cause-effect link between fly infestation and specific fungi, it is clear that the fly alters the natural microbial balance, especially the low abundant taxa. On the other hand, the most abundant ones, were not significantly influenced by the insect. In fact, despite the slight variation between the sampling locations, Aureobasidium, Cladosporium, and Alternaria, were the dominant genera, suggesting the existence of a typical olive fungal microbiome.

  • 4.
    Abdelfattah, Ahmed
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Università Mediterranea di Reggio Calabria, Italy.
    Sanzani, Simona M.
    Wisniewski, Michael
    Berg, Gabriele
    Cacciola, Santa O.
    Schena, Leonardo
    Revealing Cues for Fungal Interplay in the Plant-Air Interface in Vineyards2019Ingår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 10, artikel-id 922Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Plant-associated microorganisms play a crucial role in plant health and productivity. Belowground microbial diversity is widely reported as a major factor in determining the composition of the plant microbiome. In contrast, much less is known about the role of the atmosphere in relation to the plant microbiome. The current study examined the hypothesis that the atmospheric microbiome influences the composition of fungal communities of the aboveground organs flowers, fruit, and leaves) of table grape and vice versa. The atmosphere surrounding grape plantings exhibited a significantly higher level of fungal diversity relative to the nearby plant organs and shared a higher number of phylotypes 5,536 OTUs, 40.3%) with the plant than between organs of the same plant. Using a Bayesian source tracking approach, plant organs were determined to be the major source of the atmospheric fungal community 92%). In contrast, airborne microbiota had only a minor contribution to the grape microbiome, representing the source of 15, 4, and 35% of the fungal communities of leaves, flowers, and fruits, respectively. Moreover, data indicate that plant organs and the surrounding atmosphere shared a fraction of each other's fungal communities, and this shared pool of fungal taxa serves as a two-way reservoir of microorganisms. Microbial association analysis highlighted more positive than negative interactions between fungal phylotypes. Positive interactions were more common within the same environment, while negative interactions appeared to occur more frequently between different environments, i. e., atmosphere, leaf, flower, and fruit. The current study revealed the interplay between the fungal communities of the grape phyllosphere with the surrounding air. Plants were identified as a major source of recruitment for the atmospheric microbiome, while the surrounding atmosphere contributed only a small fraction of the plant fungal community. The results of the study suggested that the plant-air interface modulates the plant recruitment of atmospheric fungi, taking a step forward in understanding the plant holobiont assembly and how the atmosphere surrounding plants plays a role in this process. The impact of plants on the atmospheric microbiota has several biological and epidemiological implications for plants and humans.

  • 5.
    Abdelfattah, Ahmed
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Germany; Graz University of Technology, Austria .
    Tack, Ayco J. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Lobato, Carolina
    Wassermann, Birgit
    Berg, Gabriele
    From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome2023Ingår i: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 31, nr 4, s. 346-355Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host–microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.

  • 6. Abdelfattah, Ahmed
    et al.
    Tack, Ayco J. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Wasserman, Birgit
    Liu, Jia
    Berg, Gabriele
    Norelli, John
    Droby, Samir
    Wisniewski, Michael
    Evidence for host-microbiome co-evolution in apple2022Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 234, nr 6, s. 2088-2100Artikel i tidskrift (Refereegranskat)
    Abstract [en]
    • Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host–microbiome co-evolutionary dynamics are poorly understood.
    • Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species.
    • The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome.
    • This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.
  • 7.
    Abdelfattah, Ahmed
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Graz University of Technology, Austria.
    Whitehead, Susan R.
    Macarisin, Dumitru
    Liu, Jia
    Burchard, Erik
    Freilich, Shiri
    Dardick, Christopher
    Droby, Samir
    Wisniewski, Michael
    Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple2020Ingår i: Microorganisms, E-ISSN 2076-2607, Vol. 8, nr 6, artikel-id 944Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    There is growing recognition of the role that the microbiome plays in the health and physiology of many plant species. However, considerably less research has been conducted on the postharvest microbiome of produce and the impact that postharvest processing may have on its composition. Here, amplicon sequencing was used to study the effect of washing, waxing, and low-temperature storage at 2 degrees C for six months on the bacterial and fungal communities of apple calyx-end, stem-end, and peel tissues. The results of the present work reveal that tissue-type is the main factor defining fungal and bacterial diversity and community composition on apple fruit. Both postharvest treatments and low temperature storage had a strong impact on the fungal and bacterial diversity and community composition of these tissue types. Distinct spatial and temporal changes in the composition and diversity of the microbiota were observed in response to various postharvest management practices. The greatest impact was attributed to sanitation practices with major differences among unwashed, washed and washed-waxed apples. The magnitude of the differences, however, was tissue-specific, with the greatest impact occurring on peel tissues. Temporally, the largest shift occurred during the first two months of low-temperature storage, although fungi were more affected by storage time than bacteria. In general, fungi and bacteria were impacted equally by sanitation practices, especially the epiphytic microflora of peel tissues. This research provides a foundation for understanding the impact of postharvest management practices on the microbiome of apple and its potential subsequent effects on postharvest disease management and food safety.

  • 8.
    Abdelfattah, Ahmed
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Graz University of Technology, Austria.
    Wisniewski, Michael
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), USA.
    Schena, Leonardo
    Tack, Ayco J. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root2021Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 23, nr 4, s. 2199-2214Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities. 

  • 9. Abrahamczyk, S.
    et al.
    Kessler, M.
    Hanley, D.
    Karger, D. N.
    Mueller, M. P. J.
    Knauer, A. C.
    Keller, F.
    Schwerdtfeger, M.
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Imperial College London, UK.
    Pollinator adaptation and the evolution of floral nectar sugar composition2017Ingår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, nr 1, s. 112-127Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A long-standing debate concerns whether nectar sugar composition evolves as an adaptation to pollinator dietary requirements or whether it is 'phylogenetically constrained'. Here, we use a modelling approach to evaluate the hypothesis that nectar sucrose proportion (NSP) is an adaptation to pollinators. We analyse similar to 2100 species of asterids, spanning several plant families and pollinator groups (PGs), and show that the hypothesis of adaptation cannot be rejected: NSP evolves towards two optimal values, high NSP for specialist-pollinated and low NSP for generalist-pollinated plants. However, the inferred adaptive process is weak, suggesting that adaptation to PG only provides a partial explanation for how nectar evolves. Additional factors are therefore needed to fully explain nectar evolution, and we suggest that future studies might incorporate floral shape and size and the abiotic environment into the analytical framework. Further, we show that NSP and PG evolution are correlated - in a manner dictated by pollinator behaviour. This contrasts with the view that a plant necessarily has to adapt its nectar composition to ensure pollination but rather suggests that pollinators adapt their foraging behaviour or dietary requirements to the nectar sugar composition presented by the plants. Finally, we document unexpectedly sucrose-poor nectar in some specialized nectarivorous bird-pollinated plants from the Old World, which might represent an overlooked form of pollinator deception. Thus, our broad study provides several new insights into how nectar evolves and we conclude by discussing why maintaining the conceptual dichotomy between adaptation and constraint might be unhelpful for advancing this field.

  • 10. Abrahamczyk, Stefan
    et al.
    Humphreys, Aelys M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Trabert, Felix
    Droppelmann, Fabian
    Gleichmann, Maria
    Krieger, Vera
    Linnartz, Marius
    Lozada-Gobilard, Sissi
    Rahelivololona, Marie Elisette
    Schubert, Marian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Janssens, Steven B.
    Weigend, Maximilian
    Fischer, Eberhard
    Evolution of brood-site mimicry in Madagascan Impatiens (Balsaminaceae)2021Ingår i: Perspectives in plant ecology, evolution and systematics, ISSN 1433-8319, E-ISSN 1618-0437, Vol. 49, artikel-id 125590Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The species-rich flora of Madagascar is well known for a range of unusual floral ecologies. One example is Impatiens section Trimorphopetalum with its unique combination of floral traits: small, spur-less, cup-or lip shaped, greenish or brownish flowers. So far no hypotheses on floral function or pollination of this peculiar group have been proposed. We analysed six reproductive traits in relation to pollination syndromes for 34 Madagascan Impatiens species, including 18 species of section Trimorphopetalum plus six outgroup species, in a phylogenetic framework. Further, we present pollinator observations for one additional species of Trimophopetalum. All pollination syndromes occurring in the African species are also present in Madagascan Impatiens. In addition, species of Trimorphopetalum represent two unique floral types, possibly corresponding to two different types of fly pollination. The evolution of these flower types corresponds to a strong decrease in nectar production, flower display size, pollen grain and ovule number. Autogamy is found in one derived sub-clade of the otherwise largely pollinator-dependent Trimorphopetalum. We find evidence consistent with the evolution of brood-site deception and fungus mimicry in combination with fly pollination in one clade of Trimorphopetalum and the stepwise evolution of autogamy in the second clade. The evolution of these very different reproductive strategies may have been triggered by pollinator limitation in the dense, humid forest undergrowth of Madagascar.

  • 11. Abrego, Nerea
    et al.
    Huotari, Tea
    Tack, Ayco J. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Lindahl, Björn D.
    Tikhonov, Gleb
    Somervuo, Panu
    Schmidt, Niels Martin
    Ovaskainen, Otso
    Roslin, Tomas
    Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient2020Ingår i: Ecology and Evolution, E-ISSN 2045-7758, Vol. 10, nr 16, s. 8989-9002Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.

  • 12. Abrego, Nerea
    et al.
    Roslin, Tomas
    Huotari, Tea
    Tack, Ayco J. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Lindahl, Björn D.
    Tikhonov, Gleb
    Somervuo, Panu
    Schmidt, Niels Martin
    Ovaskainen, Otso
    Accounting for environmental variation in co-occurrence modelling reveals the importance of positive interactions in root-associated fungal communities2020Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 29, nr 14, s. 2736-2746Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. We generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more probably reflect interactive associations. Our results indicate that not only negative but also positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.

  • 13. Adam, Birgit
    et al.
    Klawonn, Isabell
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Svedén, Jenny B.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Bergkvist, Johanna
    Nahar, Nurun
    Walve, Jakob
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Littmann, Sten
    Whitehouse, Martin J.
    Lavik, Gaute
    Kuypers, Marcel M. M.
    Ploug, Helle
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. University of Gothenburg, Sweden.
    N2-fixation, ammonium release and N-transfer to the microbial and classical food web within a plankton community2016Ingår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, nr 2, s. 450-459Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We investigated the role of N2-fixation by the colony-forming cyanobacterium, Aphanizomenon spp., for the plankton community and N-budget of the N-limited Baltic Sea during summer by using stable isotope tracers combined with novel secondary ion mass spectrometry, conventional mass spectrometry and nutrient analysis. When incubated with 15N2Aphanizomenon spp. showed a strong 15N-enrichment implying substantial 15N2-fixation. Intriguingly, Aphanizomenon did not assimilate tracers of 15NH4+ from the surrounding water. These findings are in line with model calculations that confirmed a negligible N-source by diffusion-limited NH4+ fluxes to Aphanizomenon colonies at low bulk concentrations (<250 nm) as compared with N2-fixation within colonies. No N2-fixation was detected in autotrophic microorganisms <5 μm, which relied on NH4+uptake from the surrounding water. Aphanizomenon released about 50% of its newly fixed N2 as NH4+. However, NH4+ did not accumulate in the water but was transferred to heterotrophic and autotrophic microorganisms as well as to diatoms (Chaetoceros sp.) and copepods with a turnover time of ~5 h. We provide direct quantitative evidence that colony-formingAphanizomenon releases about half of its recently fixed N2 as NH4+, which is transferred to the prokaryotic and eukaryotic plankton forming the basis of the food web in the plankton community. Transfer of newly fixed nitrogen to diatoms and copepods furthermore implies a fast export to shallow sediments via fast-sinking fecal pellets and aggregates. Hence, N2-fixing colony-forming cyanobacteria can have profound impact on ecosystem productivity and biogeochemical processes at shorter time scales (hours to days) than previously thought.

  • 14. Adyari, Bob
    et al.
    Shen, Dandan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Leibniz Institute for Baltic Sea Research, Germany.
    Li, Shuang
    Zhang, Lanping
    Rashid, Azhar
    Sun, Qian
    Hu, Anyi
    Chen, Nengwang
    Yu, Chang-Ping
    Strong impact of micropollutants on prokaryotic communities at the horizontal but not vertical scales in a subtropical reservoir, China2020Ingår i: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 721, artikel-id 137767Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Micropollutants have become of great concern, because of their disrupting effects on the structure and function of microbial communities. However, little is known about the relative importance of trace micropollutants on the aquatic prokaryotic communities as compared to the traditional physico-chemical characteristics, especially at different spatial dimensions. Here, we investigated free-living (FL) and particle-associated (PA) prokaryotic communities in a subtropical water reservoir, China, across seasons at horizontal (surface water) and vertical (depth-profile) scales by using 16S rRNA gene amplicon sequencing. Our results showed that the shared variances of physico-chemicals and micropollutants explained majority of the spatial variations in prokaryotic communities, suggesting a strong joint effect of the two abiotic categories on reservoir prokaryotic communities. Micropollutants appeared to exert strong independent influence on the core sub-communities (i.e., abundant and wide-spread taxa) than on the satellite (i.e., less abundant and narrow-range taxa) counterparts. The pure effect of micropollutants on both core and satellite sub-communities from FL and PA fractions was similar to 1.5 folds greater than that of physico-chemical factors at the horizontal scale, whereas an opposite effect was observed at the vertical scale. Moreover, eight micropollutants including anti-fungal agents, antibiotics, bisphenol analogues, stimulant and UV-filter were identified as the major disrupting compounds with strong associations with core taxa of typical freshwater prokaryotes. Altogether, we concluded that the ecological disrupting effects of micropollutants on prokaryotic communities may vary along horizontal and vertical dimensions in freshwater ecosystems.

  • 15.
    Aguilar-Sanchez, Andrea
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Li, Jing
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Mautner, Andreas
    Jalvo, Blanca
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap.
    Pesquet, Edouard
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Mathew, Aji P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Revealing the interaction between nanopolysaccharides and E.Coli by biological studies and atomic force microscopyManuskript (preprint) (Övrigt vetenskapligt)
  • 16. Aguirrebengoa, Martin
    et al.
    Müller, Caroline
    Hambäck, Peter A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    González-Megías, Adela
    Density-Dependent Effects of Simultaneous Root and Floral Herbivory on Plant Fitness and Defense2023Ingår i: PLANTS, E-ISSN 2223-7747, Vol. 12, nr 2, artikel-id 283Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Plants are attacked by multiple herbivores, and depend on a precise regulation of responses to cope with a wide range of antagonists. Simultaneous herbivory can occur in different plant compartments, which may pose a serious threat to plant growth and reproduction. In particular, plants often face co-occurring root and floral herbivory, but few studies have focused on such interactions. Here, we investigated in the field the combined density-dependent effects of root-chewing cebrionid beetle larvae and flower-chewing pierid caterpillars on the fitness and defense of a semiarid Brassicaceae herb. We found that the fitness impact of both herbivore groups was independent and density-dependent. Increasing root herbivore density non-significantly reduced plant fitness, while the relationship between increasing floral herbivore density and the reduction they caused in both seed number and seedling emergence was non-linear. The plant defensive response was non-additive with regard to the different densities of root and floral herbivores; high floral herbivore density provoked compensatory investment in reproduction, and this tolerance response was combined with aboveground chemical defense induction when also root herbivore density was high. Plants may thus prioritize specific trait combinations in response to varying combined below- and aboveground herbivore densities to minimize negative impacts on fitness.

  • 17.
    Ahlbeck Bergendahl, Ida
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Salvanes, Anne Gro V.
    Braithwaite, Victoria A.
    Determining the effects of duration and recency of exposure to environmental enrichment2016Ingår i: Applied Animal Behaviour Science, ISSN 0168-1591, E-ISSN 1872-9045, Vol. 176, s. 163-169Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Experience can help animals adapt their behaviour to fit the environment or conditions that they find themselves in. Understanding how and when experience affects behaviour is important for the animals we rear in captivity. This is particularly true when we rear animals with the intent of releasing them into the wild as part of population rehabilitation and conservation efforts. We investigated how exposure to a changing, more complex environment promotes behavioural development in juvenile trout. Four groups of fish were compared; (i) fish that were maintained without enrichment, (ii) fish that were exposed to an early period of enrichment, but were then returned to a plain environment, (iii) fish that were maintained in plain conditions, but were then exposed to enrichment towards the end of the rearing phase, (iv) a group that were kept in enriched conditions throughout the 12 week rearing period. We then assessed fish anxiety levels, their spatial learning ability, and the capacity of the fish to find their way through a barrier where different routes were presented across 4 different trials. Fish that experienced enriched conditions for the longest duration had superior spatial learning abilities, and they were better at finding the correct route to get past the barrier than fish from the remaining three treatments. Positive effects on behaviour were, however, also found in the fish that only experienced enrichment in the last part of the rearing period, compared to the control, or fish exposed to early enrichment. No effect of enrichment was found on levels of anxiety in any of the groups.

  • 18.
    Ahmed, Engy
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Parducci, Laura
    Unneberg, Per
    Ågren, Rasmus
    Schenk, Frederik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Rattray, Jayne E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Han, Lu
    Muschitiello, Francesco
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper. Columbia University, USA.
    Pedersen, Mikkel W.
    Smittenberg, Rienk H.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Afrifa Yamoah, Kweku
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Slotte, Tanja
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Wohlfarth, Barbara
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA2018Ingår i: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 181, s. 19-29Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Lateglacial/early Holocene sediments from the ancient lake at Hasseldala Port, southern Sweden provide an important archive for the environmental and climatic shifts at the end of the last ice age and the transition into the present Interglacial. The existing multi-proxy data set highlights the complex interplay of physical and ecological changes in response to climatic shifts and lake status changes. Yet, it remains unclear how microorganisms, such as Archaea, which do not leave microscopic features in the sedimentary record, were affected by these climatic shifts. Here we present the metagenomic data set of Hasseldala Port with a special focus on the abundance and biodiversity of Archaea. This allows reconstructing for the first time the temporal succession of major Archaea groups between 13.9 and 10.8 ka BP by using ancient environmental DNA metagenomics and fossil archaeal cell membrane lipids. We then evaluate to which extent these findings reflect physical changes of the lake system, due to changes in lake-water summer temperature and seasonal lake-ice cover. We show that variations in archaeal composition and diversity were related to a variety of factors (e.g., changes in lake water temperature, duration of lake ice cover, rapid sediment infilling), which influenced bottom water conditions and the sediment-water interface. Methanogenic Archaea dominated during the Allerod and Younger Dryas pollen zones, when the ancient lake was likely stratified and anoxic for large parts of the year. The increase in archaeal diversity at the Younger Dryas/Holocene transition is explained by sediment infilling and formation of a mire/peatbog.

  • 19. Ahtiainen, Heini
    et al.
    Artell, Janne
    Elmgren, Ragnar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Hasselström, Linus
    Håkansson, Cecilia
    Baltic Sea nutrient reductions - What should we aim for?2014Ingår i: Journal of Environmental Management, ISSN 0301-4797, E-ISSN 1095-8630, Vol. 145, s. 9-23Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Nutrient load reductions are needed to improve the state of the Baltic Sea, but it is still under debate how they should be implemented. In this paper, we use data from an environmental valuation study conducted in all nine Baltic Sea states to investigate public preferences of relevance to three of the involved decision-dimensions: First, the roles of nitrogen versus phosphorus reductions causing different eutrophication effects; second, the role of time the - lag between actions to reduce nutrient loads and perceived improvements; and third; the spatial dimension and the roles of actions targeting the coastal and open sea environment and different sub-basins. Our findings indicate that respondents view and value the Baltic Sea environment as a whole, and are not focussed only on their local sea area, or a particular aspect of water quality. We argue that public preferences concerning these three perspectives should be one of the factors guiding marine policy. This requires considering the entire range of eutrophication effects, in coastal and open sea areas, and including long-term and short-term measures.

  • 20.
    Albert, Séréna
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Benthic-pelagic coupling in a changing world: Structural and functional responses of microbenthic communities to organic matter settling2021Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Marine soft sediments form the second largest habitat on the planet. Organisms residing in this environment represent a vast reservoir of biodiversity, and play key roles in ecosystem processes. Most benthic organisms depend on organic matter (OM) inputs from phytoplankton in the overlying water column as food supply, but human impacts such as eutrophication and climate change are profoundly altering natural ecosystem dynamics. The consequences of changes in benthic-pelagic coupling for the biodiversity and functioning of soft-sediment communities have yet to be resolved. 

    The aim of this thesis is to assess the role of OM settling on soft-sediments microeukaryotic (small organisms < 1 mm) and bacterial communities. The intents are two-fold, to investigate impacts on (1) community structure and diversity (chapters I, II and IV); and (2) ecosystem functioning, notably in relation to nitrogen (N) cycling (chapters I and III). 

    Our results show that settling OM quantity and quality both had a significant impact on microeukaryotic alpha-diversity. We observed a decrease in alpha-diversity following settling of diatom-derived spring bloom OM, possibly as a result of competitive exclusion, while cyanobacteria-derived summer bloom OM did not affect alpha-diversity (chapters I and IV). We also found that high biomass of diatoms and others fast sinking phytoplankton groups in the water column led to lower microeukaryotic alpha diversity after this material settled on the seafloor (chapter IV). Presumably, following this large sedimentation event, sediment oxygen (O2) demand was strongly stimulated, excluding O2-sensitive taxa. Overall, we propose that the assembly of microeukaryotic communities was primarily mediated by OM settling quantity (chapter IV), while differences in OM quality led to significant but more subtle changes, occurring at fine taxonomic level (chapter I). The response of bacterial communities to OM settling was less pronounced, and probably restricted to the uppermost sediment layer (chapters I and IV). We did, however, observe a significant effect of OM quality on bacterial communities assembly at the sediment-water interface, with taxa favored either by diatom- or by cyanobacteria-derived OM (chapter II). This study also showed that feedback mechanisms from nutrient recycling in the sediment could play a role in this response. Finally, our results indicated a substantial influence of OM quality on N cycling at the sediment-water interface. We found that settling of fresh OM (i.e. low C:N ratio) stimulated denitrification activity (chapters I and III), while simultaneously promoting more N recycling to the water column than settling of degraded OM (i.e. high C:N ratio) did (chapter III).  

    Altogether, our results indicate that current changes in OM settling dynamics in marine systems will likely impact microeukaryotic and, to some extent, bacterial biodiversity in soft sediments. Alterations in settling OM quality, in particular, may also affect crucial microbial processes involved in N cycling. This thesis highlights the importance of considering benthic-pelagic coupling mechanisms to better understand likely future changes in marine ecosystems.

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  • 21.
    Albert, Séréna
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Bonaglia, Stefano
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. University of Southern Denmark, Denmark; University of Gothenburg, Sweden.
    Stjärnkvist, Nellie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Winder, Monika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Thamdrup, Bo
    Nascimento, Francisco J. A
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Naturvetenskapliga fakulteten, Stockholms universitets Östersjöcentrum.
    Influence of settling organic matter quantity and quality on benthic nitrogen cycling2021Ingår i: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 66, nr 5, s. 1882-1895Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Coastal sediments are major contributors to global carbon (C) mineralization and nutrient cycling and are tightly linked to processes in the pelagic environment. In this study, we aimed to investigate the regulating potential of quantity and quality of planktonic organic matter (OM) deposition on benthic metabolism, with a particular focus on nitrogen (N) cycling processes. We simulated inputs of spring (C : N 10.9) and summer (C : N 5.6) plankton communities in high and low quantities to sediment cores, and followed oxygen consumption, nutrient fluxes as well as nitrate reduction rates, that is, denitrification and dissimilatory nitrate reduction to ammonium for 10 d. Our results demonstrate the primary importance of OM quality in determining the fate of organic N once it settles to the sediment surface. Settling of N-rich summer plankton material resulted in a similar to twofold lower denitrification efficiency (40-56%) compared to N-poor spring plankton (88-115%). This indicates that N-rich plankton deposition favors recycling of inorganic nutrients to the water column over N-loss via denitrification. OM quantity was positively related to mineralization activity, but this neither directly affected N fluxes nor denitrification activity, highlighting the complex interplay between the OM quantity and quality in regulating N cycling. In light of these new findings, we support the use of simple qualitative indicators such as C : N ratio of OM to investigate how future changes in benthic-pelagic coupling might influence N budgets at the sediment-water interface.

  • 22.
    Albert, Séréna
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Hedberg, Per
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Motwani, Nisha H.
    Sjöling, Sara
    Winder, Monika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Nascimento, Francisco
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communitiesManuskript (preprint) (Övrigt vetenskapligt)
  • 23.
    Albert, Séréna
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Hedberg, Per
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Motwani, Nisha H.
    Sjöling, Sara
    Winder, Monika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Nascimento, Francisco J. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Naturvetenskapliga fakulteten, Stockholms universitets Östersjöcentrum.
    Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities2021Ingår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikel-id 24033Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.

  • 24.
    Albert, Séréna
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Liénart, Camilla
    Stockholms universitet, Naturvetenskapliga fakulteten, Stockholms universitets Östersjöcentrum.
    Winder, Monika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Nascimento, Francisco
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Seasonality and drivers of microeukaryotic and bacterial communities in Baltic Sea soft sedimentsManuskript (preprint) (Övrigt vetenskapligt)
  • 25. Alcamán, M. Estrella
    et al.
    Alcorta, Jaime
    Bergman, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Vásquez, Mónica
    Polz, Martin
    Díez, Beatriz
    Physiological and gene expression responses to nitrogen regimes and temperatures in Mastigocladus sp strain CHP1, a predominant thermotolerant cyanobacterium of hot springs2017Ingår i: Systematic and Applied Microbiology, ISSN 0723-2020, E-ISSN 1618-0984, Vol. 40, nr 2, s. 102-113Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cyanobacteria are widely distributed primary producers with significant implications for the global biogeochemical cycles of carbon and nitrogen. Diazotrophic cyanobacteria of subsection V (Order Stigonematales) are particularly ubiquitous in photoautotrophic microbial mats of hot springs. The Stigonematal cyanobacterium strain CHPI isolated from the Porcelana hot spring (Chile) was one of the major contributors of the new nitrogen through nitrogen fixation. Further morphological and genetic characterization verified that the strain CHP1 belongs to Stigonematales, and it formed a separate Glade together with other thermophiles of the genera Fischerella and Mastigocladus. Strain CHP1 fixed maximum N-2 in the light, independent of the temperature range. At 50 degrees C niJH gene transcripts showed high expression during the light period, whereas the nifH gene expression at 45 degrees C was arrhythmic. The strain displayed a high affinity for nitrate and a low tolerance for high ammonium concentrations, whereas the narB and glnA genes showed higher expression in light and at the beginning of the dark phase. It is proposed that Mastigocladus sp. strain CHPI would represent a good model for the study of subsection V thermophilic cyanobacteria, and for understanding the adaptations of these photoautotrophic organisms inhabiting microbial mats in hot springs globally.

  • 26. Alexandridis, Nikolaos
    et al.
    Feit, Benjamin
    Kihara, Job
    Luttermoser, Tim
    May, Wilhelm
    Midega, Charles
    Öborn, Ingrid
    Poveda, Katja
    Sileshi, Gudeta W.
    Zewdie, Beyene
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Clough, Yann
    Jonsson, Mattias
    Climate change and ecological intensification of agriculture in sub-Saharan Africa – A systems approach to predict maize yield under push-pull technology2023Ingår i: Agriculture, Ecosystems & Environment, ISSN 0167-8809, E-ISSN 1873-2305, Vol. 352, artikel-id 108511Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Assessing effects of climate change on agricultural systems and the potential for ecological intensification to increase food security in developing countries is essential to guide management, policy-making and future research. ‘Push-pull’ technology (PPT) is a poly-cropping design developed in eastern Africa that utilizes plant chemicals to mediate plant–insect interactions. PPT application yields significant increases in crop productivity, by reducing pest load and damage caused by arthropods and parasitic weeds, while also bolstering soil fertility. As climate change effects may be species- and/or context-specific, there is need to elucidate how, in interaction with biotic factors, projected climate conditions are likely to influence future functioning of PPT. Here, we first reviewed how changes in temperature, precipitation and atmospheric CO2 concentration can influence PPT components (i.e., land use, soils, crops, weeds, diseases, pests and their natural enemies) across sub-Saharan Africa (SSA). We then imposed these anticipated responses on a landscape-scale qualitative mathematical model of maize production under PPT in eastern Africa, to predict cumulative, structure-mediated impacts of climate change on maize yield. Our review suggests variable impacts of climate change on PPT components in SSA by the end of the 21st century, including reduced soil fertility, increased weed and arthropod pest pressure and increased prevalence of crop diseases, but also increased biological control by pests’ natural enemies. Extrapolating empirical evidence of climate effects to predict responses to projected climate conditions is mainly limited by a lack of mechanistic understanding regarding single and interactive effects of climate variables on PPT components. Model predictions of maize yield responses to anticipated impacts of climate change in eastern Africa suggest predominantly negative future trends. Nevertheless, maize yields can be sustained or increased by favourable changes in system components with less certain future behaviour, including higher PPT adoption, preservation of field edge density and agricultural diversification beyond cereal crops.

  • 27.
    Alhousari, Fadi
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Greger, Maria
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Silicon and Mechanisms of Plant Resistance to Insect Pests2018Ingår i: PLANTS, E-ISSN 2223-7747, Vol. 7, nr 2, artikel-id 33Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    This paper reviews the most recent progress in exploring silicon-mediated resistance to herbivorous insects and the mechanisms involved. The aim is to determine whether any mechanism seems more common than the others as well as whether the mechanisms are more pronounced in silicon-accumulating than non-silicon-accumulating species or in monocots than eudicots. Two types of mechanisms counter insect pest attacks: physical or mechanical barriers and biochemical/molecular mechanisms (in which Si can upregulate and prime plant defence pathways against insects). Although most studies have examined high Si accumulators, both accumulators and non-accumulators of silicon as well as monocots and eudicots display similar Si defence mechanisms against insects.

  • 28. Alikas, Krista
    et al.
    Kratzer, Susanne
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Improved retrieval of Secchi depth for optically-complex waters using remote sensing data2017Ingår i: Ecological Indicators, ISSN 1470-160X, E-ISSN 1872-7034, Vol. 77, s. 218-227Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Water transparency is one of the ecological indicators for describing water quality and the underwater light field which determines its productivity. In the European Water Framework Directive (WFD) as well as in the European Marine Strategy Framework Directive (MSFD) water transparency is used for ecological status classification of inland, coastal and open sea waters and it is regarded as an indicator for eutrophication in Baltic Sea management (HELCOM, 2007). We developed and compared different empirical and semi-analytical algorithms for lakes and coastal Nordic waters to retrieve Secchi depth (Z(SD)) from remote sensing data (MERIS, 300 m resolution).The algorithms were developed in water bodies with high coloured dissolved organic matter absorption (a(CNOM)(442) ranging 1.7-4.0 m(-1)), Chl a concentration (0.5-73 mg m(-3)) and total suspended matter (0.7-37.5 g m(-3)) and validated against an independent data set over inland and coastal waters (0.6 m < Z(SD) < 14.8 m). The results indicate that for empirical algorithms, using longer wavelengths in the visible spectrum as a reference band decreases the RMSE and increases the coefficient of determination (R-2). The accuracy increased (R-2 = 0.75, RMSE = 1.33 m, n = 134) when Z(SD) was retrieved via an empirical relationship between Z(SD) and K-d (490). The best agreement with in situ data was attained when Z(SD) was calculated via both the diffuse and the beam attenuation coefficient (R-2 = 0.89, RMSE = 0.77 m, n = 89). The results demonstrate that transparency can be retrieved with high accuracy over various optical water types by the means of ocean color remote sensing, improving both the spatial and temporal coverage. The satellite derived Z(SD) product could be therefore used as an additional source of information for WFD and MSFD reporting purposes.

  • 29. Alikas, Krista
    et al.
    Kratzer, Susanne
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Brockmann Consult GmbH, Geesthacht, Germany.
    Reinart, Anu
    Kauer, Tuuli
    Paavel, Birgot
    Robust remote sensing algorithms to derive the diffuse attenuation coefficient for lakes and coastal waters2015Ingår i: Limnology and Oceanography: Methods, E-ISSN 1541-5856, Vol. 13, nr 8, s. 402-415Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this study, empirical and semianalytical algorithms are developed and compared for optically complex waters to retrieve the diffuse attenuation coefficient of downwelling irradiance (Kd(lambda)) from satellite data. In the first approach, a band ratio algorithm was used. Various sets of MERIS band ratios were tested to achieve the best estimates for K-d(490) based on the in situ dataset which was measured in Nordic lakes (oligotrophic to eutrophic conditions). In the second approach, K-d(490) was expressed as a function of inherent optical properties which were retrieved from MERIS standard products. The algorithms from both approaches were tested against an independent data set and validated in optically complex coastal waters in the Baltic Sea and in Nordic lakes with high concentrations of coloured dissolved organic matter (0.3 < a(cdom)(442) m(-1) < 4.5), chlorophyll a (Chl a) (0.7< C-Chl a(mg m(-3))< 67.5) and total suspended matter (TSM) (0.5 < C-TSM(g m(-3)) < 26.4). MERIS-derived K-d(490) values showed reliable estimates in case of both methods. The results indicate that for band ratio algorithms, the root mean square error (RMSE) decreases and the coefficient of determination (R-2) increases when using longer wavelengths in the visible spectrum as a reference band. It was found that the best estimates were retrieved from MERIS data when using the ratio of R-rs(490)/R-rs(709) for coastal waters (K-d(490) < 2.5 m(-1)) and the ratio R-rs(560)/R-rs(709) for more turbid inland waters (Kd(490) > 2.5 m(-1)). As a result, a combined band ratio algorithm was developed, which provides a promising approach R-2 = 0.98, RMSE= 17%, N = 34, p < 0.05) for estimating K-d(490) over a wide range of values (0.3-6.1 m(-1)).

  • 30. Allen, Lisa Zeigler
    et al.
    McCrow, John P.
    Ininbergs, Karolina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Dupont, Christopher L.
    Badger, Jonathan H.
    Hoffman, Jeffery M.
    Ekman, Martin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Allen, Andrew E.
    Bergman, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Venter, J. Craig
    The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses2017Ingår i: mSystems, E-ISSN 2379-5077, Vol. 2, nr 1, artikel-id UNSP e00125-16Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Tornetrask in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Tornetrask. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.

  • 31. Alneberg, Johannes
    et al.
    Bennke, Christin
    Beier, Sara
    Bunse, Carina
    Quince, Christopher
    Ininbergs, Karolina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Riemann, Lasse
    Ekman, Martin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Jürgens, Klaus
    Labrenz, Matthias
    Pinhassi, Jarone
    Andersson, Anders F.
    Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes2020Ingår i: Communications Biology, E-ISSN 2399-3642, Vol. 3, nr 1, artikel-id 119Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes. The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.

  • 32.
    Alonso Aller, Elisa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Effects of Marine Protected Areas on Tropical Seagrass Ecosystems2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Seagrass beds are highly productive coastal ecosystems that sustain a rich and diverse associated fauna and flora. Increasing anthropogenic pressures threaten seagrass ecosystems and have already led to major seagrass losses across the world. Marine Protected Areas (MPAs) have become one of the key strategies to manage coastal ecosystems and associated resources worldwide and have been often shown to successfully protect marine ecosystems. However, relatively few studies have assessed the effects of MPAs on seagrass ecosystems, and there are indications that MPAs may not be able to fully protect seagrasses, especially from disturbances originating outside their boundaries. Within this context, this thesis aimed to investigate the direct and indirect effects (those mediated by biotic interactions) of MPAs on tropical seagrasses, associated fish communities, and ecosystem processes.

    The thesis consists of three parts. First, we used 10-years of seagrass monitoring data within a MPA to evaluate the temporal variability in seagrass cover and species composition in relation to changes in environmental conditions (Paper I). Second, we investigated the potential of MPAs to enhance the temporal stability of seagrass ecosystems using a 10-month field study. We surveyed seagrass-associated fish communities (Paper II) and estimated seagrass growth and herbivory rates (Paper III) during three different seasons within MPAs and unprotected sites. Finally, to evaluate the effects of MPAs and land-use on seagrass ecosystems we surveyed seagrass species and trait composition within government-managed MPAs, community-managed MPAs, and unprotected sites (Paper IV).

    The seagrass bed monitored in Paper I showed a high temporal and spatial variability, with a temporal decline in cover and change in species composition, followed by a period of recovery. This pattern could not be associated with any of the climate and tidal variables considered, suggesting that potential drivers of decline may have originated outside MPA boundaries. The results from the seasonal field study showed that MPAs increased the temporal stability of seagrass-associated fish communities, particularly juvenile fish (Paper II), and strengthened a positive link between herbivorous fish, herbivory rates, and seagrass growth (Paper III), suggesting the presence of a positive feedback that promotes stability. Finally, MPAs affected seagrass species and trait composition (by selecting for more stress-sensitive species) but did not seem to be able to protect seagrasses from land-use effects, with seagrasses showing similar changes in species and trait composition within and outside MPAs (Paper IV). Considering these results, this thesis builds to a body of literature indicating that MPAs alone may not be sufficient to protect seagrass ecosystems and that improved management strategies may be necessary to preserve these important coastal habitats.

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  • 33.
    Alonso Aller, Elisa
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Eklöf, Johan S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Gullström, Martin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. University of Gothenburg, Sweden.
    Kloiber, U.
    Linderholm, H. W.
    Nordlund, L. M.
    Temporal variability of a protected multispecific tropical seagrass meadow in response to environmental change2019Ingår i: Environmental Monitoring & Assessment, ISSN 0167-6369, E-ISSN 1573-2959, Vol. 191, nr 12, artikel-id 774Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In a changing environment, there is an increasing interest to monitor ecosystems to understand their responses to environmental change. Seagrass meadows are highly important ecosystems that are under constant pressure from human activities and climate impacts, with marked declines observed worldwide. Despite increasing efforts, monitoring of multispecific tropical seagrass meadows is scarce, particularly in low-income regions. Based on data from a monitoring programme in a marine protected area in Zanzibar (Tanzania), we assessed temporal changes in seagrass cover and species composition during a 10-year period in relation to local variability in environmental variables. We observed a strong, gradual decline in seagrass cover and changes in species composition, followed by a period of recovery. However, the timing and length of these temporal patterns varied in space (between transects). Multiple environmental variables-cloud cover, temperature, storm occurrence, sunspot activity, and tidal amplitude and height-influenced seagrass cover, although only to a minor extent, suggesting that the monitored seagrass meadow may be influenced by other unmeasured factors (e.g. water currents and sediment movement). Our results show that seagrass meadows can be highly dynamic at small (10-50 m) spatial scales, even in the absence of major local anthropogenic impacts. Our findings suggest that high-resolution monitoring programmes can be highly valuable for the detection of temporal changes in multispecific seagrass meadows; however, to understand the causes of change, there is a need of long-term (> 10 years) data series that include direct measurements of environmental variables and extreme events.

  • 34.
    Alonso Aller, Elisa
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Eklöf, Johan S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Gullström, Martin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Kloiber, Ulrike
    Linderholm, Hans W.
    Nordlund, Lina M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Monitoring of a protected multi-specific tropical seagrass meadow reveals a pattern of decline and recoveryManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    In a changing environment, there is an increasing interest to monitor ecosystems to understand their responses to environmental change. Seagrass meadows are highly important ecosystems, but at the same time they are under a constant threat from human activities, as well as climate impacts, and marked declines have been observed worldwide. Despite increasing efforts, monitoring of multi-specific tropical seagrass meadows is scarce, particularly in developing regions. Here we analysed data from the first 10 years of a monitoring programme in a marine protected area in Zanzibar (Tanzania) to assess temporal changes in seagrass cover and species composition and to detect potential drivers of change. The seagrass meadow experienced a strong gradual decline in seagrass cover and changes in species composition, followed by a period of recovery. However, the timing and length of these temporal patterns varied in space (between transects). Of the climate variables considered, cloud cover, temperature, storm occurrence, sunspot activity and the height of the diurnal low tide seemed to influence seagrass cover, although only to a small extent, suggesting that the monitored seagrass meadow may be influenced by other unmeasured factors. Considering our results, seagrass meadows seem to be highly dynamic at small spatial scales even in the absence of major local anthropogenic impacts. Further monitoring programmes should be developed in the region to gain a better understanding of seagrass temporal variability and causes of change.

  • 35.
    Alonso Aller, Elisa
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Gullström, Martin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Eveleens Maarse, Floriaan K. J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Gren, Michaela
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Nordlund, Lina Mtwana
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. WIO CARE, Zanzibar, Tanzania.
    Jiddawi, Narriman
    Eklöf, Johan S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Single and joint effects of regional- and local-scale variables on tropical seagrass fish assemblages2014Ingår i: Marine Biology, ISSN 0025-3162, E-ISSN 1432-1793, Vol. 161, nr 10, s. 2395-2405Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Seagrass beds are highly important for tropical ecosystems by supporting abundant and diverse fish assemblages that form the basis for artisanal fisheries. Although a number of local- and regional-scale variables are known to influence the abundance, diversity and assemblage structure of seagrass-associated fish assemblages, few studies have evaluated the relative and joint (interacting) influences of variables, especially those acting at different scales. Here, we examined the relative importance of local- and regional-scale factors structuring seagrass-associated fish assemblages, using a field survey in six seagrass (Thalassodendron ciliatum) areas around Unguja Island (Zanzibar, Tanzania). Fish density and assemblage structure were mostly affected by two regional-scale variables; distance to coral reefs, which positively affected fish density, and level of human development, which negatively affected fish density. On the local scale, seagrass biomass had a positive (but weaker) influence on fish density. However, the positive effect of seagrass biomass decreased with increasing level of human development. In summary, our results highlight the importance of assessing how multiple local and regional variables, alone and together, influence fish communities, in order to improve management of seagrass ecosystems and their services.

  • 36.
    Alonso Aller, Elisa
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Jiddawi, Narriman S.
    Eklöf, Johan S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Fishing weakens a positive link between herbivore abundance and plant growth in tropical seagrass bedsManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Herbivory is a key process influencing the structure and function of both terrestrial and aquatic systems. In seagrass ecosystems, moderate levels of herbivory may stimulate plant growth, compensating for the loss of eaten tissue. However, the relationship between herbivory and seagrass growth can be influenced by an array of factors, such as seasonality, herbivore abundance, and presence of epiphytes, many of which can be directly or indirectly affected by human activities like fishing. Here, we used data from a multi-season field survey in fished and protected seagrass beds to assess how fishing and seasonality affect the link between herbivores, herbivory, and plant growth in seagrasses. Path analyses revealed an interactive effect of seasonality and protection. In protected seagrass beds, seasonally high herbivore abundance positively affected herbivory rates, which in turn enhanced seagrass growth. This link was however not apparent in seagrass beds subjected to fishing activities. At the same time, seasonality effects seemed stronger in fished areas, suggesting that in addition to weakening a positive herbivory-plant growth interaction, fishing increases temporal instability of ecosystems. Our results highlight the need for evaluating not only the direct effects of fisheries exploitation on fish populations, but also the potential indirect effects on ecosystems, to improve fisheries management.

  • 37.
    Alonso Aller, Elisa
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Jiddawi, Narriman S.
    Eklöf, Johan S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Marine protected areas increase temporal stability of community structure, but not density or diversity, of tropical seagrass fish communities2017Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 12, nr 8, artikel-id e0183999Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Marine protected areas (MPAs) have been shown to increase long-term temporal stability of fish communities and enhance ecosystem resilience to anthropogenic disturbance. Yet, the potential ability of MPAs to buffer effects of environmental variability at shorter time scales remains widely unknown. In the tropics, the yearly monsoon cycle is a major natural force affecting marine organisms in tropical regions, and its timing and severity are predicted to change over the coming century, with potentially severe effects on marine organisms, ecosystems and ecosystem services. Here, we assessed the ability of MPAs to buffer effects of monsoon seasonality on seagrass-associated fish communities, using a field survey in two MPAs (no-take zones) and two unprotected (open-access) sites around Zanzibar (Tanzania). We assessed the temporal stability of fish density and community structure within and outside MPAs during three monsoon seasons in 2014-2015, and investigated several possible mechanisms that could regulate temporal stability. Our results show that MPAs did not affect fish density and diversity, but that juvenile fish densities were temporally more stable within MPAs. Second, fish community structure was more stable within MPAs for juvenile and adult fish, but not for subadult fish or the total fish community. Third, the observed effects may be due to a combination of direct and indirect (seagrass-mediated) effects of seasonality and, potentially, fluctuating fishing pressure outside MPAs. In summary, these MPAs may not have the ability to enhance fish density and diversity and to buffer effects of monsoon seasonality on the whole fish community. However, they may increase the temporal stability of certain groups, such as juvenile fish. Consequently, our results question whether MPAs play a general role in the maintenance of biodiversity and ecosystem functioning under changing environmental conditions in tropical seagrass fish communities.

  • 38. Alonzo, Frederic
    et al.
    Hertel-Aas, Turid
    Real, Almudena
    Lance, Emilie
    Garcia-Sanchez, Laurent
    Bradshaw, Clare
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Vives i Baffle, Jordi
    Oughton, Deborah H.
    Garnier-Laplace, Jacqueline
    Population modelling to compare chronic external radiotoxicity between individual and population endpoints in four taxonomic groups2016Ingår i: Journal of Environmental Radioactivity, ISSN 0265-931X, E-ISSN 1879-1700, Vol. 152, s. 46-59Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this study, we modelled population responses to chronic external gamma radiation in 12 laboratory species (including aquatic and soil invertebrates, fish and terrestrial mammals). Our aim was to compare radiosensitivity between individual and population endpoints and to examine how internationally proposed benchmarks for environmental radioprotection protected species against various risks at the population level. To do so, we used population matrix models, combining life history and chronic radiotoxicity data (derived from laboratory experiments and described in the literature and the FRED ERICA database) to simulate changes in population endpoints (net reproductive rate R-0, asymptotic population growth rate lambda, equilibrium population size N-eq) for a range of dose rates. Elasticity analyses of models showed that population responses differed depending on the affected individual endpoint (juvenile or adult survival, delay in maturity or reduction in fecundity), the considered population endpoint (R-0, lambda or N-eq) and the life history of the studied species. Among population endpoints, net reproductive rate R-0 showed the lowest EDR10 (effective dose rate inducing 10% effect) in all species, with values ranging from 26 mu Gy h(-1) in the mouse Mus musculus to 38,000 mu Gy h(-1) in the fish Oryzias latipes. For several species, EDR10 for population endpoints were lower than the lowest EDR10 for individual endpoints. Various population level risks, differing in severity for the population, were investigated. Population extinction (predicted when radiation effects caused population growth rate lambda to decrease below 1, indicating that no population growth in the long term) was predicted for dose rates ranging from 2700 mu Gy h(-1) in fish to 12,000 mu Gy h(-1) in soil invertebrates. A milder risk, that population growth rate lambda will be reduced by 10% of the reduction causing extinction, was predicted for dose rates ranging from 24 mu Gy h(-1) in mammals to 1800 mu Gy h(-1) in soil invertebrates. These predictions suggested that proposed reference benchmarks from the literature for different taxonomic groups protected all simulated species against population extinction. A generic reference benchmark of 10 mu Gy h(-1) protected all simulated species against 10% of the effect causing population extinction. Finally, a risk of pseudo-extinction was predicted from 2.0 mu Gy h(-1) in mammals to 970 mu Gy h(-1) in soil invertebrates, representing a slight but statistically significant population decline, the importance of which remains to be evaluated in natural settings.

  • 39.
    Ament-Velásquez, Sandra Lorena
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen, Avdelningen för populationsgenetik.
    Vogan, Aaron A.
    Wallerman, Ola
    Hartmann, Fanny E.
    Gautier, Valerie
    Silar, Philippe
    Giraud, Tatiana
    Johannesson, Hanna
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex2024Ingår i: Genome Biology and Evolution, E-ISSN 1759-6653, Vol. 16, nr 3, artikel-id evae034Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.

  • 40.
    Amid, C.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Olstedt, M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Gunnarsson, Jonas S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Le Lan, H.
    Tran Thi Minh, H.
    Van den Brink, P. J.
    Hellström, M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Tedengren, Michael
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Additive effects of the herbicide glyphosate and elevated temperature on the branched coral Acropora formosa in Nha Trang, Vietnam2018Ingår i: Environmental Science and Pollution Research, ISSN 0944-1344, E-ISSN 1614-7499, Vol. 25, nr 14, s. 13360-13372Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The combined effects of the herbicide glyphosate and elevated temperature were studied on the tropical staghorn coral Acropora formosa, in Nha Trang bay, Vietnam. The corals were collected from two different reefs, one close to a polluted fish farm and one in a marine-protected area (MPA). In the laboratory, branches of the corals were exposed to the herbicide glyphosate at ambient (28 degrees C) and at 3 degrees C elevated water temperatures (31 degrees C). Effects of herbicide and elevated temperature were studied on coral bleaching using photography and digital image analysis (new colorimetric method developed here based on grayscale), chlorophyll a analysis, and symbiotic dinoflagellate (Symbiodinium, referred to as zooxanthellae) counts. All corals from the MPA started to bleach in the laboratory before they were exposed to the treatments, indicating that they were very sensitive, as opposed to the corals collected from the more polluted site, which were more tolerant and showed no bleaching response to temperature increase or herbicide alone. However, the combined exposure to the stressors resulted in significant loss of color, proportional to loss in chlorophyll a and zooxanthellae. The difference in sensitivity of the corals collected from the polluted site versus the MPA site could be explained by different symbiont types: the resilient type C3u and the stress-sensitive types C21 and C23, respectively. The additive effect of elevated temperatures and herbicides adds further weight to the notion that the bleaching of coral reefs is accelerated in the presence of multiple stressors. These results suggest that the corals in Nha Trang bay have adapted to the ongoing pollution to become more tolerant to anthropogenic stressors, and that multiple stressors hamper this resilience. The loss of color and decrease of chlorophyll a suggest that bleaching is related to concentration of chloro-pigments. The colorimetric method could be further fine-tuned and used as a precise, non-intrusive tool for monitoring coral bleaching in situ.

  • 41. Amienl, Aldine R.
    et al.
    Johnston, Hereroa
    Chock, Taylor
    Dahlin, Paul
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Iglesias, Marta
    Layden, Michael
    Röttinger, Eric
    Martindale, Mark Q.
    A bipolar role of the transcription factor ERG for cnidarian germ layer formation and apical domain patterning2017Ingår i: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 430, nr 2, s. 346-361Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Germ layer formation and axial patterning are biological processes that are tightly linked during embryonic development of most metazoans. In addition to canonical WNT, it has been proposed that ERK-MAPK signaling is involved in specifying oral as well as aboral territories in cnidarians. However, the effector and the molecular mechanism underlying latter phenomenon is unknown. By screening for potential effectors of ERK-MAPK signaling in both domains, we identified a member of the ETS family of transcription factors, Nverg that is bipolarily expressed prior to gastrulation. We further describe the crucial role of NvERG for gastrulation, endomesoderm as well as apical domain formation. The molecular characterization of the obtained NvERG knock-down phenotype using previously described as well as novel potential downstream targets, provides evidence that a single transcription factor, NvERG, simultaneously controls expression of two different sets of downstream targets, leading to two different embryonic gene regulatory networks (GRNs) in opposite poles of the developing embryo. We also highlight the molecular interaction of cWNT and MEK/ERK/ERG signaling that provides novel insight into the embryonic axial organization of Nematostella, and show a cWNT repressive role of MEK/ERK/ERG signaling in segregating the endomesoderm in two sub-domains, while a common input of both pathways is required for proper apical domain formation. Taking together, we build the first blueprint for a global cnidarian embryonic GRN that is the foundation for additional gene specific studies addressing the evolution of embryonic and larval development.

  • 42.
    An, Yueqing
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Braga, Mariana P.
    Garcia, Sarahi L.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Grudzinska-Sterno, Magdalena
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Hambäck, Peter A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles2023Ingår i: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 86, nr 4, s. 2477-2487Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Gut microbes play important roles for their hosts. Previous studies suggest that host-microbial systems can form long-term associations over evolutionary time and the dynamic changes of the intestinal system may represent major driving forces and contribute to insect dietary diversification and speciation. Our study system includes a set of six closely related leaf beetle species (Galerucella spp.) and our study aims to separate the roles of host phylogeny and ecology in determining the gut microbial community and to identify eventual relationship between host insects and gut bacteria. We collected adult beetles from their respective host plants and quantified their microbial community using 16S rRNA sequencing. The results showed that the gut bacteria community composition was structured by host beetle phylogeny, where more or less host-specific gut bacteria interact with the different Galerucella species. For example, the endosymbiotic bacteria Wolbachia was found almost exclusively in G. nymphaea and G. sagittariae. Diversity indicators also suggested that α- and β-diversities of gut bacteria communities varied among host beetle species. Overall, our results suggest a phylogenetically controlled co-occurrence pattern between the six closely related Galerucella beetles and their gut bacteria, indicating the potential of co-evolutionary processes occurring between hosts and their gut bacterial communities. 

  • 43.
    Anderson, Benjamin M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Krause, Kirsten
    Petersen, Gitte
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmF(C) genes2021Ingår i: BMC Genomics, E-ISSN 1471-2164, Vol. 22, nr 1, artikel-id 816Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus.

    Results: The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmF(C) gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT.

    Conclusions: The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.

  • 44. Andersson, A.
    et al.
    Brugel, S.
    Paczkowska, J.
    Rowe, O. F.
    Figueroa, D.
    Kratzer, Susanne
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Legrand, C.
    Influence of allochthonous dissolved organic matter on pelagic basal production in a northerly estuary2018Ingår i: Estuarine, Coastal and Shelf Science, ISSN 0272-7714, E-ISSN 1096-0015, Vol. 204, s. 225-235Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Phytoplankton and heterotrophic bacteria are key groups at the base of aquatic food webs. In estuaries receiving riverine water with a high content of coloured allochthonous dissolved organic matter (ADOM), phytoplankton primary production may be reduced, while bacterial production is favoured. We tested this hypothesis by performing a field study in a northerly estuary receiving nutrient-poor, ADOM-rich riverine water, and analyzing results using multivariate statistics. Throughout the productive season, and especially during the spring river flush, the production and growth rate of heterotrophic bacteria were stimulated by the riverine inflow of dissolved organic carbon (DOC). In contrast, primary production and photosynthetic efficiency (i.e. phytoplankton growth rate) were negatively affected by DOC. Primary production related positively to phosphorus, which is the limiting nutrient in the area. In the upper estuary where DOC concentrations were the highest, the heterotrophic bacterial production constituted almost 100% of the basal production (sum of primary and bacterial production) during spring, while during summer the primary and bacterial production were approximately equal. Our study shows that riverine DOC had a strong negative influence on coastal phytoplankton production, likely due to light attenuation. On the other hand DOC showed a positive influence on bacterial production since it represents a supplementary food source. Thus, in boreal regions where climate change will cause increased river inflow to coastal waters, the balance between phytoplankton and bacterial production is likely to be changed, favouring bacteria. The pelagic food web structure and overall productivity will in turn be altered.

  • 45. Andersson, Agneta
    et al.
    Höglander, Helena
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Karlsson, Chatarina
    Huseby, Siv
    Key role of phosphorus and nitrogen in regulating cyanobacterial community composition in the northern Baltic Sea2015Ingår i: Estuarine, Coastal and Shelf Science, ISSN 0272-7714, E-ISSN 1096-0015, Vol. 164, s. 161-171Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Despite cyanobacteria being a key phytoplankton group in the Baltic Sea, the factors governing their community structure are still poorly understood. Here, we studied the occurrence of the orders Chroococcales, Oscillatoriales and Nostocales, and potentially explanatory variables at five locations in the northern Baltic Sea from June September, 1998-2012. Cyanobacteria constituted 1-36% of the total phytoplankton biomass along the north south gradient. In the Bothnian Bay, Chroococcales and Oscillatoriales dominated the cyanobacterial community, whereas in the Bothnian Sea and northern Baltic Proper, Nostocales was the dominant group. The dominance of Chroococcales was coupled to low salinity and low total phosphorus, whereas Oscillatoriales correlated with high total nitrogen and low salinity. Nostocales correlated to high total phosphorus, inorganic phosphorus and salinity. Chroococcales showed an increase over time in the offshore Bothnian Bay, whereas Nostocales increased in the coastal Bothnian Sea and coastal Baltic Proper. The increase of Nostocales in the coastal Bothnian Sea was explained by a rise in total phosphorus and decrease in dissolved inorganic nitrogen compared to an increase of total nitrogen and phosphorus in the coastal Baltic Proper. No significant trends were observed in the cyanobacterial community in the offshore Bothnian Sea and the offshore northern Baltic Proper. We concluded that Chroococcales may be a useful indicator for increased phosphorus levels in waters with low phosphorus concentrations, whereas Nostocales could be used as a quality indicator for increasing phosphorus concentrations in waters with low inorganic N/P ratios (< 20), such as in the coastal Bothnian Sea and Baltic Proper.

  • 46. Andersson, Agneta
    et al.
    Meier, H. E. Markus
    Ripszam, Matyas
    Rowe, Owen
    Wikner, Johan
    Haglund, Peter
    Eilola, Kari
    Legrand, Catherine
    Figueroa, Daniela
    Paczkowska, Joanna
    Lindehoff, Elin
    Tysklind, Mats
    Elmgren, Ragnar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Projected future climate change and Baltic Sea ecosystem management2015Ingår i: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 44, s. S345-S356Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Climate change is likely to have large effects on the Baltic Sea ecosystem. Simulations indicate 2-4 degrees C warming and 50-80 % decrease in ice cover by 2100. Precipitation may increase similar to 30 % in the north, causing increased land runoff of allochthonous organic matter (AOM) and organic pollutants and decreased salinity. Coupled physical-biogeochemical models indicate that, in the south, bottom-water anoxia may spread, reducing cod recruitment and increasing sediment phosphorus release, thus promoting cyanobacterial blooms. In the north, heterotrophic bacteria will be favored by AOM, while phytoplankton production may be reduced. Extra trophic levels in the food web may increase energy losses and consequently reduce fish production. Future management of the Baltic Sea must consider the effects of climate change on the ecosystem dynamics and functions, as well as the effects of anthropogenic nutrient and pollutant load. Monitoring should have a holistic approach, encompassing both autotrophic (phytoplankton) and heterotrophic (e.g., bacterial) processes.

  • 47.
    Andersson, Erik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Stockholm Resilience Centre. North-West University, South Africa.
    Boonstra, Wiebren J.
    de la Torre Castro, Maricela
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Hughes, Alice C.
    Ilstedt, Ulrik
    Jernelöv, Arne
    Jonsson, Bengt-Gunnar
    Kalantari, Zahra
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi. KTH Royal Institute of Technology, Sweden.
    Keskitalo, Carina
    Kritzberg, Emma
    Kätterer, Thomas
    McNeely, Jeffrey A.
    Mohr, Claudia
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap.
    Mustonen, Tero
    Ostwald, Madelene
    Reyes-Garcia, Victoria
    Rusch, Graciela M.
    Sanderson Bellamy, Angelina
    Stage, Jesper
    Tedengren, Michael
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Thomas, David N.
    Wulff, Angela
    Söderström, Bo
    Ambio fit for the 2020s2022Ingår i: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 51, nr 5, s. 1091-1093Artikel i tidskrift (Övrigt vetenskapligt)
  • 48.
    Andersson, Petter
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Ehrlén, Johan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Hambäck, Peter A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Plant patch structure influences plant fitness via antagonistic and mutualistic interactions but in different directions2016Ingår i: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 180, nr 4, s. 1175-1182Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Plant patch structure and environmental context can influence the outcome of antagonistic and mutualistic plant-insect interactions, leading to spatially variable fitness effects for plants. We investigated the effects of herbivory and pollen limitation on plant reproductive performance in 28 patches of the self-compatible perennial herb Scrophularia nodosa and assessed how such effects varied with plant patch size, plant density and tree cover. Both antagonistic and mutualistic interactions had strong effects on plant reproductive performance. Leaf feeding from herbivores reduced both fruit production and seed germination, and leaf herbivory increased with plant patch size. Experimentally hand-pollinated flowers produced more seeds than open-pollinated flowers, and pollen limitation was more severe in patches with fewer plants. Our study on S. nodosa is one of few which documents that plant patch structure influences the outcome of both antagonistic and mutualistic plant-insect interactions. The results thus provide an example of how variation in plant patch structure and environmental factors can lead to spatially variable fitness effects from mutualistic and antagonistic interactions.

  • 49.
    Andersson, Petter
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Löfstedt, Christer
    Lund Univ, Dept Biol..
    Hambäck, Peter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Insect density-plant density relationships: a modified view of insect responses to resource concentrations2013Ingår i: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 173, nr 4, s. 1333-1344Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Habitat area is an important predictor of spatial variation in animal densities. However, the area often correlates with the quantity of resources within habitats, complicating our understanding of the factors shaping animal distributions. We addressed this problem by investigating densities of insect herbivores in habitat patches with a constant area but varying numbers of plants. Using a mathematical model, predictions of scale-dependent immigration and emigration rates for insects into patches with different densities of host plants were derived. Moreover, a field experiment was conducted where the scaling properties of odour-mediated attraction in relation to the number of odour sources were estimated, in order to derive a prediction of immigration rates of olfactory searchers. The theoretical model predicted that we should expect immigration rates of contact and visual searchers to be determined by patch area, with a steep scaling coefficient, mu = -1. The field experiment suggested that olfactory searchers should show a less steep scaling coefficient, with mu a parts per thousand -0.5. A parameter estimation and analysis of published data revealed a correspondence between observations and predictions, and density-variation among groups could largely be explained by search behaviour. Aphids showed scaling coefficients corresponding to the prediction for contact/visual searchers, whereas moths, flies and beetles corresponded to the prediction for olfactory searchers. As density responses varied considerably among groups, and variation could be explained by a certain trait, we conclude that a general theory of insect responses to habitat heterogeneity should be based on shared traits, rather than a general prediction for all species.

  • 50.
    Andersson, Petter
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Löfstedt, Christer
    Hambäck, Peter A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    How insects sense olfactory patches: the spatial scaling of olfactory information2013Ingår i: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 122, nr 7, s. 1009-1016Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    When searching for resources in heterogeneous environments, animals must rely on their abilities to detect the resources via their sensory systems. However, variation in the strength of the sensory cue may be mediated by the physical size of the resource patch. Patch detection of insects are often predicted by the scaling of sensory cues to patch size, where visual cues has been proposed to scale proportional to the diameter of the patch. The scaling properties of olfactory cues are, however, virtually unknown. Here, we investigated scaling rules for olfactory information in a gradient of numbers of odour sources, relevant to odour-mediated attraction under field conditions. We recorded moth antennal responses to sex pheromones downwind from pheromone patches and estimated the slope in the scaling relationship between the effective length of the odour plumes and the number of odour sources. These measurements showed that the effective plume length increased proportional to the square root of the number of odour sources. The scaling relationship, as estimated in the field experiment, was then evaluated against field data of the slope in the relationship between trap catch and release rate of chemical attractants for a wide range of insects. This meta-analysis revealed an average slope largely consistent with the estimated scaling relationship between the effective plume length and the number of odour sources. This study is the first to estimate the scaling properties of olfactory cues empirically and has implications for understanding and predicting the spatial distributions of insects searching by means of olfactory cues in heterogeneous environments.

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