scholarly journals Rewetting of Three Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes Through Environmental Filtering

2019 ◽  
Author(s):  
Micha Weil ◽  
Haitao Wang ◽  
Mia Bengtsson ◽  
Daniel Köhn ◽  
Anke Günther ◽  
...  
Keyword(s):  
Community Composition ◽  
Ecosystem Respiration ◽  
Abiotic Factors ◽  
Environmental Filtering ◽  
Network Analyses ◽  
Respiration Rates ◽  
Control Community ◽  
Methane Fluxes ◽  
Compositional Changes ◽  
Shed Light

AbstractDrained peatlands are significant sources of the greenhouse gas (GHG) carbon dioxide. Rewetting is a proven strategy to protect carbon stocks; however, it can lead to increased emissions of the potent GHG methane. The response to rewetting of soil microbiomes as drivers of these processes is poorly understood, as are biotic and abiotic factors that control community composition.We analyzed the pro- and eukaryotic microbiomes of three contrasting pairs of minerotrophic fens subject to decade-long drainage and subsequent rewetting. Also, abiotic soil properties including moisture, dissolved organic matter, methane fluxes and ecosystem respiration rates.The composition of the microbiomes was fen-type-specific, but all rewetted sites showed higher abundance of anaerobic taxa compared to drained sites. Based on multi-variate statistics and network analyses we identified soil moisture as major driver of community composition. Furthermore, salinity drove the separation between coastal and freshwater fen communities. Methanogens were more than tenfold more abundant in rewetted than in drained sites, while their abundance was lowest in the coastal fen, likely due to competition with sulfate reducers. The microbiome compositions were reflected in methane fluxes from the sites. Our results shed light on the factors that structure fen microbiomes via environmental filtering.

scholarly journals Rewetting of Three Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering

2020 ◽  
Author(s):  
Micha Weil ◽  
Haitao Wang ◽  
Mia Bengtsson ◽  
Daniel Köhn ◽  
Anke Günther ◽  
...  
Keyword(s):  
Community Composition ◽  
Ecosystem Respiration ◽  
Abiotic Factors ◽  
Environmental Filtering ◽  
Network Analyses ◽  
Respiration Rates ◽  
Control Community ◽  
Methane Fluxes ◽  
Compositional Changes ◽  
Shed Light

Drained peatlands are significant sources of the greenhouse gas (GHG) carbon dioxide. Rewetting is a proven strategy to protect carbon stocks; however, it can lead to increased emissions of the potent GHG methane. The response to rewetting of soil microbiomes as drivers of these processes is poorly understood, as are biotic and abiotic factors that control community composition. We analyzed the pro- and eukaryotic microbiomes of three contrasting pairs of minerotrophic fens subject to decade-long drainage and subsequent rewetting. Also, abiotic soil properties including moisture, dissolved organic matter, methane fluxes and ecosystem respiration rates. The composition of the microbiomes was fen-type-specific, but all rewetted sites showed higher abundance of anaerobic taxa compared to drained sites. Based on multi-variate statistics and network analyses we identified soil moisture as major driver of community composition. Furthermore, salinity drove the separation between coastal and freshwater fen communities. Methanogens were more than tenfold more abundant in rewetted than in drained sites, while their abundance was lowest in the coastal fen, likely due to competition with sulfate reducers. The microbiome compositions were reflected in methane fluxes from the sites. Our results shed light on the factors that structure fen microbiomes via environmental filtering.

scholarly journals Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering

2020 ◽  
Vol 8 (4) ◽  
pp. 550 ◽  
Author(s):  
Micha Weil ◽  
Haitao Wang ◽  
Mia Bengtsson ◽  
Daniel Köhn ◽  
Anke Günther ◽  
...  
Keyword(s):  
Community Composition ◽  
Ecosystem Respiration ◽  
Abiotic Factors ◽  
Environmental Filtering ◽  
Network Analyses ◽  
Control Community ◽  
Methane Fluxes ◽  
Compositional Changes ◽  
Shed Light

Drained peatlands are significant sources of the greenhouse gas (GHG) carbon dioxide. Rewetting is a proven strategy used to protect carbon stocks; however, it can lead to increased emissions of the potent GHG methane. The response to rewetting of soil microbiomes as drivers of these processes is poorly understood, as are the biotic and abiotic factors that control community composition. We analyzed the pro- and eukaryotic microbiomes of three contrasting pairs of minerotrophic fens subject to decade-long drainage and subsequent long-term rewetting. Abiotic soil properties including moisture, dissolved organic matter, methane fluxes, and ecosystem respiration rates were also determined. The composition of the microbiomes was fen-type-specific, but all rewetted sites showed higher abundances of anaerobic taxa compared to drained sites. Based on multi-variate statistics and network analyses, we identified soil moisture as a major driver of community composition. Furthermore, salinity drove the separation between coastal and freshwater fen communities. Methanogens were more than 10-fold more abundant in rewetted than in drained sites, while their abundance was lowest in the coastal fen, likely due to competition with sulfate reducers. The microbiome compositions were reflected in methane fluxes from the sites. Our results shed light on the factors that structure fen microbiomes via environmental filtering.

scholarly journals Assembly processes of gastropod community change with horizontal and vertical zonation in ancient Lake Ohrid: a metacommunity speciation perspective

2016 ◽  
Vol 13 (10) ◽  
pp. 2901-2911 ◽  
Author(s):  
Torsten Hauffe ◽  
Christian Albrecht ◽  
Thomas Wilke
Keyword(s):  
Community Composition ◽  
Community Assembly ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Species Interaction ◽  
Relative Importance ◽  
Lake Depth ◽  
Ancient Lake ◽  
Lake Ohrid ◽  
Speciation Model

Abstract. The Balkan Lake Ohrid is the oldest and most diverse freshwater lacustrine system in Europe. However, it remains unclear whether species community composition, as well as the diversification of its endemic taxa, is mainly driven by dispersal limitation, environmental filtering, or species interaction. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics, as provided by the unifying framework of the “metacommunity speciation model”.The current study used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process-based metacommunity analyses. Specifically, the study aimed (1) to identifying the relative importance of the three community assembly processes and (2) to test whether the importance of these individual processes changes gradually with lake depth or discontinuously with eco-zone shifts.Based on automated eco-zone detection and process-specific simulation steps, we demonstrated that dispersal limitation had the strongest influence on gastropod community composition. However, it was not the exclusive assembly process, but acted together with the other two processes – environmental filtering and species interaction. The relative importance of the community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter.This suggests that environmental characteristics have a pronounced effect on shaping gastropod communities via assembly processes. Moreover, the study corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community composition) and generating endemic biodiversity (via its influence on diversification processes). However, according to the metacommunity speciation model, the inferred importance of environmental filtering and biotic interaction also suggests a small but significant influence of ecological speciation. These findings contribute to the main goal of the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) deep drilling initiative – inferring the drivers of biotic evolution – and might provide an integrative perspective on biological and limnological dynamics in ancient Lake Ohrid.

scholarly journals Seasonal and annual variation of carbon fluxes in a young Siberian larch (<i>Larix sibirica</i>) plantation in Iceland

2009 ◽  
Vol 6 (4) ◽  
pp. 6601-6634 ◽  
Author(s):  
B. Bjarnadottir ◽  
B. D. Sigurdsson ◽  
A. Lindroth
Keyword(s):  
Carbon Balance ◽  
Climatic Factors ◽  
Ecosystem Respiration ◽  
Abiotic Factors ◽  
Gross Primary Production ◽  
Seasonal Pattern ◽  
Soil Water Potential ◽  
Siberian Larch ◽  
Frost Damage ◽  
Spring Frost

Abstract. This study reports 3-year measurements (2004–2006) of net ecosystem exchange (NEE) over a 12–14 year old Siberian larch forest in Iceland established on previously grazed heath land pasture that had been site-prepared prior to planting. The study evaluated interannual and seasonal variation of NEE and its component fluxes, gross primary production (GPP) and ecosystem respiration (Re), with the aim to clarify how climatic factors controlled the site's carbon balance. The young plantation acted as a relatively strong sink for CO2 during all of the three years, with a net sequestration of −375, −566 and −245 g CO2 m−2 for years 2004, 2005 and 2006, respectively. The annual carbon balance was strongly influenced by climatic factors leading to a high inter-annual variability in NEE. This variation was more related to variation in carbon efflux (Re) than carbon uptake (GPP). The abiotic factors that showed the strongest correlation to Re were air temperature during the growing season and soil water potential. The GPP mostly followed the seasonal pattern in irradiance, except in 2005, when the plantation experienced severe spring frost damage that set the GPP back to zero. It was not expected that the rather slow-growing Siberian larch plantation would be such a strong sink for atmospheric CO2 only twelve years after site preparation and afforestation.

scholarly journals Differential arthropod responses to warming are altering the structure of Arctic communities

2018 ◽  
Vol 5 (4) ◽  
pp. 171503 ◽  
Author(s):  
Amanda M. Koltz ◽  
Niels M. Schmidt ◽  
Toke T. Høye
Keyword(s):  
Community Composition ◽  
Primary Productivity ◽  
Species Interactions ◽  
Ecosystem Processes ◽  
The Arctic ◽  
Individual Species ◽  
Freeze Thaw ◽  
Compositional Changes ◽  
Arctic Communities

The Arctic is experiencing some of the fastest rates of warming on the planet. Although many studies have documented responses to such warming by individual species, the idiosyncratic nature of these findings has prevented us from extrapolating them to community-level predictions. Here, we leverage the availability of a long-term dataset from Zackenberg, Greenland (593 700 specimens collected between 1996 and 2014), to investigate how climate parameters influence the abundance of different arthropod groups and overall community composition. We find that variation in mean seasonal temperatures, winter duration and winter freeze–thaw events is correlated with taxon-specific and habitat-dependent changes in arthropod abundances. In addition, we find that arthropod communities have exhibited compositional changes consistent with the expected effects of recent shifts towards warmer active seasons and fewer freeze–thaw events in NE Greenland. Changes in community composition are up to five times more extreme in drier than wet habitats, with herbivores and parasitoids generally increasing in abundance, while the opposite is true for surface detritivores. These results suggest that species interactions and food web dynamics are changing in the Arctic, with potential implications for key ecosystem processes such as decomposition, nutrient cycling and primary productivity.

scholarly journals Soil Microbial Biomass and Community Composition Relates to Poplar Genotypes and Environmental Conditions

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 262 ◽  
Author(s):  
Leszek Karliński ◽  
Sabine Ravnskov ◽  
Maria Rudawska
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Community Composition ◽  
Soil Depth ◽  
Abiotic Factors ◽  
Soil Conditions ◽  
Main Role ◽  
Site Factors ◽  
Host Genotype ◽  
The Impact

Poplars, known for their diversity, are trees that can develop symbiotic relationships with several groups of microorganisms. The genetic diversity of poplars and different abiotic factors influence the properties of the soil and may shape microbial communities. Our study aimed to analyse the impact of poplar genotype on the biomass and community composition of the microbiome of four poplar genotypes grown under different soil conditions and soil depths. Of the three study sites, established in the mid-1990s, one was near a copper smelter, whereas the two others were situated in unpolluted regions, but were differentiated according to the physicochemical traits of the soil. The whole-cell fatty acid analysis was used to determine the biomass and proportions of gram-positive, gram-negative and actinobacteria, arbuscular fungi (AMF), other soil fungi, and protozoa in the whole microbial community in the soil. The results showed that the biomass of microorganisms and their contributions to the community of organisms in the soil close to poplar roots were determined by both factors: the tree-host genotype and the soil environment. However, each group of microorganisms was influenced by these factors to a different degree. In general, the site effect played the main role in shaping the microbial biomass (excluding actinobacteria), whereas tree genotype determined the proportions of the fungal and bacterial groups in the microbial communities and the proportion of AMF in the fungal community. Bacterial biomass was influenced more by site factors, whereas fungal biomass more by tree genotype. With increasing soil depth, a decrease in the biomass of all microorganisms was observed; however, the proportions of the different microorganisms within the soil profile were the result of interactions between the host genotype and soil conditions. Despite the predominant impact of soil conditions, our results showed the important role of poplar genotype in shaping microorganism communities in the soil.

scholarly journals Outlier Detection for Minor Compositional Variations in Taxonomic Abundance Data

2019 ◽  
Vol 9 (7) ◽  
pp. 1355
Author(s):  
Koji Ishiya ◽  
Sachiyo Aburatani
Keyword(s):  
Microbial Communities ◽  
Natural Environments ◽  
Human Gut ◽  
Short Term ◽  
Computational Framework ◽  
Dietary Changes ◽  
Compositional Changes ◽  
Compositional Variations ◽  
Living Organisms ◽  
Shed Light

To understand the activities of complex microbial communities in various natural environments and living organisms, we need to capture the compositional changes in their taxonomic abundance. Here, we propose a new computational framework to detect compositional changes in microorganisms, including minor bacteria. This framework is designed to statistically assess relative variations in taxonomic abundance. By using this approach, we detected compositional changes in the human gut microbiome that might be associated with short-term human dietary changes. Our approach can shed light on the compositional changes of minor microorganisms that are easily overlooked.

scholarly journals The roles of environmental variation and spatial distance in explaining diversity and biogeography of soil denitrifying communities in remote Tibetan wetlands

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Xiaoliang Jiang ◽  
Wenzhi Liu ◽  
Lunguang Yao ◽  
Guihua Liu ◽  
Yuyi Yang
Keyword(s):  
Electrical Conductivity ◽  
Soil Moisture ◽  
Soil Temperature ◽  
Community Composition ◽  
Environmental Filtering ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Spatial Distance ◽  
Wetland Type ◽  
Α Diversity

ABSTRACT The relative importance of local environments and dispersal limitation in shaping denitrifier community structure remains elusive. Here, we collected soils from 36 riverine, lacustrine and palustrine wetland sites on the remote Tibetan Plateau and characterized the soil denitrifier communities using high-throughput amplicon sequencing of the nirS and nirK genes. Results showed that the richness of nirS-type denitrifiers in riverine wetlands was significantly higher than that in lacustrine wetlands but not significantly different from that in palustrine wetlands. There was no clear distinction in nir community composition among the three kinds of wetlands. Irrespective of wetland type, the soil denitrification rate was positively related to the abundance, but not the α-diversity, of denitrifying communities. Soil moisture, carbon availability and soil temperature were the main determinants of diversity [operational taxonomic unit (OTU) number] and abundance of thenirS-type denitrifier community, while water total organic carbon, soil NO3– and soil moisture were important in controlling nirK-type denitrifier diversity and abundance. The nirS community composition was influenced by water electrical conductivity, soil temperature and water depth, while the nirK community composition was affected by soil electrical conductivity. Spatial distance explained more variation in the nirS community composition than in the nirK community composition. Our findings highlight the importance of both environmental filtering and spatial distance in explaining diversity and biogeography of soil nir communities in remote and relatively undisturbed wetlands.

Nitrogen fixation beyond leguminous plants: characterising overlooked plant-bacteria associations in the light of climate change

2020 ◽  
Author(s):  
Kathrin Rousk
Keyword(s):  
Climate Change ◽  
Nitrogen Fixation ◽  
Community Composition ◽  
Abiotic Factors ◽  
Arctic Tundra ◽  
The Arctic ◽  
Mean Annual Precipitation ◽  
Precipitation Gradient ◽  
Cyanobacterial Community ◽  
Moss Species

&lt;p&gt;Nitrogen (N&lt;sub&gt;2&lt;/sub&gt;) fixation performed by moss-associated cyanobacteria is one of the main sources of new N in pristine, high latitude ecosystems like boreal forests and arctic tundra. Here, mosses and associated cyanobacteria can contribute more than 50% to total ecosystem N input. However, N&lt;sub&gt;2&lt;/sub&gt; fixation in mosses is strongly influenced by abiotic factors, in particular moisture and temperature. Hence, climate change will significantly affect this key ecosystem process in pristine ecosystems. Here,&amp;#160;I will present a synthesis of several field and laboratory assessments of moss-associated N&lt;sub&gt;2&lt;/sub&gt; fixation in response to climate change by manipulating moisture and temperature in subarctic and arctic tundra.&lt;/p&gt;&lt;p&gt;Both in a long-term climate warming experiment in the arctic, and along a continental climate gradient, spanning arctic, subarctic and temperate ecosystems, increased temperatures (up to 30 &amp;#176;C) lead to either no effect or decreased N&lt;sub&gt;2&lt;/sub&gt; fixation rates in different moss species. Yet, N&lt;sub&gt;2&lt;/sub&gt; fixation rates were strongly dependent on moss-moisture, which seems to be a more important driver of N&lt;sub&gt;2&lt;/sub&gt; fixation in mosses than temperature.&lt;/p&gt;&lt;p&gt;In another set of studies, two dominant moss species (Hylocomium splendens, Pleurozium schreberi) were collected from a steep precipitation gradient (400-1200 mm mean annual precipitation, MAP) in the Subarctic close to Abisko, Northern Sweden, and were incubated at different moisture and temperature levels in the laboratory. Nitrogen fixation, cyanobacterial abundance (via qPCR) and cyanobacterial community composition (via sequencing) on the mosses were assessed. Moisture and temperature interacted strongly to control moss-associated N&lt;sub&gt;2&lt;/sub&gt; fixation rates, and the highest activity was found at the wet end of the precipitation gradient. Although cyanobacterial abundance was higher in one of the investigated mosses (H. splendens), translating into higher N&lt;sub&gt;2&lt;/sub&gt; fixation rates, cyanobacterial community composition did not differ between the two moss species. Nostoc was the most common cyanobacterial genera on both mosses, and hardly any methanotrophic N&lt;sub&gt;2&lt;/sub&gt; fixing bacteria were found on the mosses along the precipitation gradient. Increased temperatures lead to increased abundances of certain cyanobacterial genera (Cylindrospermum and Nostoc), while others declined in response to warming. Hence, cyanobacterial communities colonizing mosses will be dominated by a few cyanobacteria species in a warmer climate, and temperature and moisture interact strongly to affect their activity. Thus, these two major climate change factors should be considered in unison when estimating climate change effects on key ecosystem processes such as N&lt;sub&gt;2&lt;/sub&gt; fixation. Further, host identity determines cyanobacterial abundance, and thereby, N&lt;sub&gt;2&lt;/sub&gt; fixation rates.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;

From a conceptual framework to an operational approach for managing grassland functional diversity to obtain targeted ecosystem services: Case studies from French mountains

2013 ◽  
Vol 29 (3) ◽  
pp. 239-254 ◽  
Author(s):  
M. Duru ◽  
C. Jouany ◽  
X. Le Roux ◽  
M.L. Navas ◽  
P. Cruz
Keyword(s):  
Ecosystem Services ◽  
Conceptual Framework ◽  
Community Composition ◽  
Functional Traits ◽  
Management Practices ◽  
Abiotic Factors ◽  
Microbial Community Composition ◽  
Operational Approach ◽  
Functional Perspective ◽  
Functional Types

AbstractResearch to understand and manage ecosystems to supply services has recently spurred a functional view of their biodiversity. In particular, approaches based on functional traits rather than species diversity are increasingly used to reflect interactions between organisms and their environment. These approaches bring a functional perspective to the study of community structure responses to disturbances and resources, and of their effects on ecosystem functioning and services. From an academic perspective, we propose a conceptual framework based on species functional traits to better infer how grassland management practices (fertilization, defoliation regime) along with abiotic factors influence plant, animal and microbial community composition and a range of services in grassland ecosystems. The core of the framework relies on combinations of plant functional traits and associated microbial features that specifically respond to environmental and management factors and influence ecosystem services. To overcome stakeholders’ difficulty in applying the concept of functional traits, we propose an operational approach implying the mapping of plant communities distributed into five plant functional types (PFTs). The approach was used for fields in grassland-based livestock farms from two French grassland networks. We evaluated its ability to predict a range of services including forage provision and non-market services according to environmental and management drivers. PFT-based plant community composition predicted forage services reasonably well but responded weakly to environmental gradients. To cope with the observed limitations of current predictive approaches, we suggest including soil microbial functional types and adaptive management rather than using a prescriptive scheme.

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