scholarly journals Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake

2020 ◽  
Author(s):  
Gwendoline M. David ◽  
David Moreira ◽  
Guillaume Reboul ◽  
Nataliia V. Annenkova ◽  
Luis J. Galindo ◽  
...  
Keyword(s):  
Climate Change ◽  
Community Structure ◽  
Microbial Community ◽  
Lake Baikal ◽  
Latitudinal Gradient ◽  
Biotic Interactions ◽  
Open Water ◽  
Freshwater Lake ◽  
Significant Difference ◽  
Vertical Gradients

SummaryIdentifying which abiotic and biotic factors determine microbial community assembly is crucial to understand ecological processes and predict how communities will respond to environmental change. While global surveys aim at addressing this question in the world’s oceans, equivalent studies in large freshwater systems are virtually lacking. Being the oldest, deepest and most voluminous freshwater lake on Earth, Lake Baikal offers a unique opportunity to test the effect of horizontal versus vertical gradients in community structure. Here, we characterized the structure of planktonic microbial eukaryotic communities (0.2-30 µm cell size) along a North-South latitudinal gradient (∼600 km) from samples collected in coastal and pelagic waters and from surface to the deepest zones (5-1400 m) using an 18S rRNA gene metabarcoding approach. Our results show complex and diverse protist communities dominated by alveolates (ciliates and dinoflagellates), ochrophytes and holomycotan lineages, with cryptophytes, haptophytes, katablepharids and telonemids in moderate abundance and many low-frequency lineages, including several typical marine members, such as diplonemids, syndinians and radiolarians. Depth had a strong significant effect on protist community stratification. By contrast, the effect of the latitudinal gradient was marginal and no significant difference was observed between coastal and surface open water communities. Co-occurrence network analyses showed that epipelagic communities are much more interconnected than meso- and bathypelagic communities and suggest specific biotic interactions between autotrophic, heterotrophic and parasitic lineages that influence protist community structure. Since climate change is rapidly affecting Siberia and Lake Baikal, our comprehensive protist survey constitutes a useful reference to monitor ongoing community shifts.Originality and Significance StatementLake Baikal is the oldest, deepest and most voluminous freshwater lake on Earth, offering a unique opportunity to test the effects of horizontal versus vertical gradients on microbial community structure. Using a metabarcoding approach, we studied planktonic microbial eukaryotes from Baikal water columns (5 up to 1,400 m depth) across a North-South latitudinal gradient (∼600 km), including coastal and pelagic areas. Our results show that depth has a strong effect on protist community assemblage, but not latitude (minor effect) or coastal vs. open water sites (no effect). Co-occurrence analyses also point to specific biotic interactions as drivers of community structure. This comprehensive survey constitutes a useful reference for monitoring active climate change effects in this ancient lake.

Environmental drivers of plankton and sediment microbial communities along latitudinal and vertical gradients in the deepest freshwater lake (Baikal, Southern Siberia)

2021 ◽  
Author(s):  
Purificacion Lopez-Garcia ◽  
Guillaume Reboul ◽  
Gwendoline David ◽  
Ludwig Jardillier ◽  
Nataliia Annenkova ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Water Column ◽  
Lake Baikal ◽  
Latitudinal Gradient ◽  
Benthic Communities ◽  
Freshwater Lake ◽  
Metabolic Potential ◽  
Significant Difference ◽  
Water Columns ◽  
Vertical Gradients

<p>Understanding how abiotic and biotic factors influence microbial community assembly and function is crucial to understand ecological processes and predict how communities will respond to environmental change. Lake Baikal (Russian Federation) is the oldest, deepest and most voluminous freshwater lake on Earth, resembling in several respects sea environments. It thus offers a unique opportunity to test the effect of horizontal versus vertical gradients in community structure. Since climate change is rapidly affecting Siberia and Lake Baikal, this information can be useful both, as a reference for future monitoring of the lake and to help predictions about how local communities change as a function of environmental parameters. In order to address these questions, in 2017, we carried out a comprehensive sampling of Lake Baikal water columns and sediments along a North–South latitudinal gradient (ca. 600 km) across the three major basins of the lake, from coastal to pelagic areas and from surface to the deepest zones (0.5 to 1450 m deep). We then applied metabarcoding approaches based on 16S and 18S rRNA gene amplicon sequencing to characterize the composition of microbial communities, in particular, both prokaryotes and eukaryotes in sediments and microbial eukaryotes (0.2-30 µm cell size) in plankton (65 samples from 17 water columns). As expected, depth had a strong significant effect on protist community stratification in the water column. The effect of the latitudinal gradient was marginal and no significant difference was observed between coastal and surface open water communities. Co-occurrence network analyses showed that epipelagic protist communities were significantly more interconnected than in the dark water column. Surprisingly, Baikal benthic communities (13 sites) displayed remarkable stability across sites and seemed not determined by depth or latitude. Comparative analyses with other freshwater, brackish and marine sediments confirmed the distinctness of Baikal benthic communities, which show some similarity to marine and hydrothermally-influenced systems likely owing to its high oligotrophy, depth and fault-associated seepage. Metagenomic analyses of sediment samples show a wide metabolic potential of Baikal benthos and highlight the relative importance ammonia-oxidizing archaea in upper sediment layers.</p>

Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal

2011 ◽  
Vol 79 (2) ◽  
pp. 348-358 ◽  
Author(s):  
Vitaly V. Kadnikov ◽  
Andrey V. Mardanov ◽  
Alexey V. Beletsky ◽  
Olga V. Shubenkova ◽  
Tatiana V. Pogodaeva ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Lake Baikal ◽  
Microbial Community Structure ◽  
Methane Hydrate ◽  
Freshwater Lake ◽  
Hydrate Bearing Sediments

scholarly journals Plant genotype controls wetland soil microbial functioning in response to sea-level rise

2021 ◽  
Vol 18 (23) ◽  
pp. 6133-6146
Author(s):  
Hao Tang ◽  
Susanne Liebner ◽  
Svenja Reents ◽  
Stefanie Nolte ◽  
Kai Jensen ◽  
...  
Keyword(s):  
Climate Change ◽  
Community Structure ◽  
Microbial Community ◽  
Sea Level Rise ◽  
Sea Level ◽  
Microbial Community Structure ◽  
Soil Microbial Communities ◽  
Litter Breakdown ◽  
Plant Genotype ◽  
Soil Microbial

Abstract. Climate change can strongly alter soil microbial functioning via plant–microbe interactions, often with important consequences for ecosystem carbon and nutrient cycling. Given the high degree of intraspecific trait variability in plants, it has been hypothesized that genetic shifts within plant species yield a large potential to control the response of plant–microbe interactions to climate change. Here we examined if sea-level rise and plant genotype interact to affect soil microbial communities in an experimental coastal wetland system, using two known genotypes of the dominant salt-marsh grass Elymus athericus characterized by differences in their sensitivity to flooding stress – i.e., a tolerant genotype from low-marsh environments and an intolerant genotype from high-marsh environments. Plants were exposed to a large range of flooding frequencies in a factorial mesocosm experiment, and soil microbial activity parameters (exo-enzyme activity and litter breakdown) and microbial community structure were assessed. Plant genotype mediated the effect of flooding on soil microbial community structure and determined the presence of flooding effects on exo-enzyme activities and belowground litter breakdown. Larger variability in microbial community structure, enzyme activities, and litter breakdown in soils planted with the intolerant plant genotype supported our general hypothesis that effects of climate change on soil microbial activity and community structure can depend on plant intraspecific genetic variation. In conclusion, our data suggest that adaptive genetic variation in plants could suppress or facilitate the effects of sea-level rise on soil microbial communities. If this finding applies more generally to coastal wetlands, it yields important implications for our understanding of ecosystem–climate feedbacks in the coastal zone.

Formation and succession of microbial community structure in different ecological niches under reclaimed water acclimation

2020 ◽  
Author(s):  
Jie Li ◽  
Yujiao Sun ◽  
Xiaoyu Wang ◽  
Meng Yin ◽  
Shangwei Xu
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Water Resources ◽  
Natural Water ◽  
Reclaimed Water ◽  
Ecological Niches ◽  
Community Structures ◽  
Significant Difference ◽  
Microbial Community Structures ◽  
The Difference

<p>Using reclaimed water as a resource for landscape water replenishment may alleviate the major problems of water resource shortages and water environment pollution. However, the safety of the water and the risk of eutrophication remain doubted by the public. Our study aimed to reveal the difference between natural water and reclaimed water and to discuss the rationality of reclaimed water replenishment from the perspective of microorganisms. We analyzed the microbial community structures in natural water, reclaimed water and natural biofilms and the community succession was clarified along the ecological niches, water resources, liquidity and time using 16S rRNA gene amplicon sequencing. Primary biofilms without the original community were added to study the formation of microbial community structures under reclaimed water acclimation. The results showed that the difference caused by ecological niches was more than those caused by the liquidity of water and different water resources. No significant difference was found in the microbial diversity and community structure caused by the addition of reclaimed water. Based on the microbial analysis, reclaimed water replenishment is a feasible solution that can be used for supplying river water. Innovatively, we introduced the study of biofilms and determined that the monitoring of biofilms or sediments closely related to water was also important for the early warning of water bloom, providing a unique perspective for the management of eutrophication.</p>

Response of soil microbial biomass, activities, and community structure at a pine stand in northeastern Germany 5 years after thinning

2006 ◽  
Vol 36 (6) ◽  
pp. 1427-1434 ◽  
Author(s):  
Sebastian Maassen ◽  
Hannu Fritze ◽  
Stephan Wirth
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Microbial Community Structure ◽  
Basal Respiration ◽  
Organic Layer ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Significant Difference ◽  
Northeastern Germany

A thinned and an unthinned treatment were compared in a 62-year-old pine stand located in northeastern Germany (Brandenburg, Ost-Prignitz, Revier Beerenbusch) (year of thinning: 1999, degree of canopy opening: 0.4). Samples of the organic layer (O) and the mineral horizon (Aeh) of an acid brown earth were collected along a transect at each treatment in November 2003 and April 2004. Substrate induced respiration, basal respiration, and a suite of enzymes involved in the degradation of lignocellulose (endocellulase, exocellulase, β-glucosidase, endoxylanase, exoxylanase, phenoloxidase, peroxidase) were assayed. Microbial community structure and relative biomass of bacteria, actinomycetes, and fungi were assayed by phospholipid fatty acid analysis. Five years after thinning, microbial biomass, basal respiration, and enzyme activities in both soil layers did not differ significantly between thinned and unthinned treatments. However, the analysis of soil microbial community structure revealed a significant difference between the thinned and unthinned treatment at both sampling dates. Thus, it was concluded that thinning had not yet resulted in any response in soil microbial activities at the site under study, but since early evidence of change in the microbial community was detected, long-term monitoring and additional studies on mineralization activities are required.

Bacterial and Archaeal Community Structure in the Surface Diatom Sediments of Deep Freshwater Lake Baikal (Eastern Siberia)

2018 ◽  
Vol 35 (8) ◽  
pp. 635-647 ◽  
Author(s):  
Yulia R. Zakharova ◽  
Darya P. Petrova ◽  
Yuri P. Galachyants ◽  
Maria V. Bashenkhaeva ◽  
Maria I. Kurilkina ◽  
...  
Keyword(s):  
Community Structure ◽  
Lake Baikal ◽  
Archaeal Community ◽  
Freshwater Lake ◽  
Eastern Siberia

scholarly journals The Effects of Artificially Dosed Adult Rumen Contents on Abomasum Transcriptome and Associated Microbial Community Structure in Calves

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 424
Author(s):  
Naren Gaowa ◽  
Wenli Li ◽  
Brianna Murphy ◽  
Madison Cox
Keyword(s):  
Community Structure ◽  
Immune System ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Molecular Mechanisms ◽  
High Efficiency ◽  
Rumen Content ◽  
System Process ◽  
Significant Difference ◽  
Immune System Process

This study aimed to investigate the changes in abomasum transcriptome and the associated microbial community structure in young calves with artificially dosed, adult rumen contents. Eight young bull calves were randomly dosed with freshly extracted rumen contents from an adult cow (high efficiency (HE), n = 4), or sterilized rumen content (Con, n = 4). The dosing was administered within 3 days of birth, then at 2, 4, and 6 weeks following the initial dosing. Abomasum tissues were collected immediately after sacrifice at 8 weeks of age. Five genera (Tannerella, Desulfovibrio, Deinococcus, Leptotrichia, and Eubacterium; P < 0.05) showed significant difference in abundance between the treatments. A total of 975 differentially expressed genes were identified (P < 0.05, fold-change > 1.5, mean read-counts > 5). Pathway analysis indicated that up-regulated genes were involved in immune system process and defense response to virus, while the down-regulated genes involved in ion transport, ATP biosynthetic process, and mitochondrial electron transport. Positive correlation (r > 0.7, P < 0.05) was observed between TRPM4 gene and Desulfovibrio, which was significantly higher in the HE group. TRPM4 had a reported role in the immune system process. In conclusion, the dosing of adult rumen contents to calves can alter not only the composition of active microorganisms in the abomasum but also the molecular mechanisms in the abomasum tissue, including reduced protease secretion and decreased hydrochloric acid secretion.

scholarly journals Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Rebecca J. Stevick ◽  
Anton F. Post ◽  
Marta Gómez-Chiarri
Keyword(s):  
Climate Change ◽  
Community Structure ◽  
Ecosystem Services ◽  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Community Structure ◽  
Environmental Conditions ◽  
Eastern Oyster ◽  
Coastal Pollution ◽  
And Function

Abstract Background Oysters in coastal environments are subject to fluctuating environmental conditions that may impact the ecosystem services they provide. Oyster-associated microbiomes are responsible for some of these services, particularly nutrient cycling in benthic habitats. The effects of climate change on host-associated microbiome composition are well-known, but functional changes and how they may impact host physiology and ecosystem functioning are poorly characterized. We investigated how environmental parameters affect oyster-associated microbial community structure and function along a trophic gradient in Narragansett Bay, Rhode Island, USA. Adult eastern oyster, Crassostrea virginica, gut and seawater samples were collected at 5 sites along this estuarine nutrient gradient in August 2017. Samples were analyzed by 16S rRNA gene sequencing to characterize bacterial community structures and metatranscriptomes were sequenced to determine oyster gut microbiome responses to local environments. Results There were significant differences in bacterial community structure between the eastern oyster gut and water samples, suggesting selection of certain taxa by the oyster host. Increasing salinity, pH, and dissolved oxygen, and decreasing nitrate, nitrite and phosphate concentrations were observed along the North to South gradient. Transcriptionally active bacterial taxa were similar for the different sites, but expression of oyster-associated microbial genes involved in nutrient (nitrogen and phosphorus) cycling varied throughout the Bay, reflecting the local nutrient regimes and prevailing environmental conditions. Conclusions The observed shifts in microbial community composition and function inform how estuarine conditions affect host-associated microbiomes and their ecosystem services. As the effects of estuarine acidification are expected to increase due to the combined effects of eutrophication, coastal pollution, and climate change, it is important to determine relationships between host health, microbial community structure, and environmental conditions in benthic communities.

scholarly journals Climate variability and drought modulate the role of structural refuges for arthropods: a global experiment

2021 ◽  
Author(s):  
Gustavo Romero ◽  
Thiago Gonçalves-Souza ◽  
Tomas Roslin ◽  
Robert Marquis ◽  
Nicholas Marino ◽  
...  
Keyword(s):  
Climate Change ◽  
Climate Variability ◽  
Latitudinal Gradient ◽  
Climatic Variability ◽  
Biotic Interactions ◽  
Predator Diversity ◽  
Terrestrial Arthropods ◽  
Geographic Regions ◽  
The Impact

Current climate change is disrupting biotic interactions and eroding biodiversity worldwide. However, species sensitive to drought, high temperatures and climate variability might persist in microclimatic refuges, such as leaf shelters built by arthropods. We conducted a distributed experiment across an 11,790 km latitudinal gradient to explore how the importance of leaf shelters for terrestrial arthropods changes with latitude, elevation and underlying climate. Our analyses revealed leaf shelters to be key facilitative elements for the diversity of arthropods. Predator diversity and overall biomass within shelters increased with local drought and temperature variability, regardless of latitude and elevation. In contrast, shelter usage by herbivores increased with abundance of predators on those same plants and in wetter climates. Projected increase in climatic variability and drought in certain geographic regions is therefore likely to enhance the importance of biotic refuges, especially for predators, in mitigating the impact of climate change on species persistence.

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