Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake

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.

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Controls on soil microbial community stability under climate change

Frontiers in Microbiology ◽

10.3389/fmicb.2013.00265 ◽

2013 ◽

Vol 4 ◽

Cited By ~ 164

Author(s):

Franciska T. de Vries ◽

Ashley Shade

Keyword(s):

Climate Change ◽

Microbial Community ◽

Soil Microbial Community ◽

Community Stability ◽

Soil Microbial

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

Environmental Microbiology ◽

10.1111/1462-2920.15346 ◽

2020 ◽

Author(s):

Gwendoline M. David ◽

David Moreira ◽

Guillaume Reboul ◽

Nataliia V. Annenkova ◽

Luis J. Galindo ◽

...

Keyword(s):

Freshwater Lake ◽

Environmental Drivers ◽

Vertical Gradients

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

FEMS Microbiology Ecology ◽

10.1111/j.1574-6941.2011.01221.x ◽

2011 ◽

Vol 79 (2) ◽

pp. 348-358 ◽

Cited By ~ 55

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

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Microbial Community Resilience across Ecosystems and Multiple Disturbances

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.00026-20 ◽

2021 ◽

Vol 85 (2) ◽

Author(s):

Laurent Philippot ◽

Bryan S. Griffiths ◽

Silke Langenheder

Keyword(s):

Microbial Community ◽

Global Environmental Change ◽

Terrestrial Ecosystems ◽

Ecosystem Functions ◽

Community Stability ◽

Multiple Disturbances ◽

Rates Of Change ◽

Complex Processes ◽

Global Environmental ◽

Nonadditive Effects

SUMMARY The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. However, despite global environmental change consisting of numerous pressures, it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions. This is particularly the case for those multiple or compounded disturbances that occur more frequently than the normal recovery time. The aim of this review is to provide an overview of the mechanisms that can govern the responses of microbes to multiple disturbances across aquatic and terrestrial ecosystems. We first summarize and discuss properties and mechanisms that influence resilience in aquatic and soil biomes to determine whether there are generally applicable principles. Following, we focus on interactions resulting from inherent characteristics of compounded disturbances, such as the nature of the disturbance, timing, and chronology that can lead to complex and nonadditive effects that are modulating the response of microorganisms.

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Multifactorial diversity sustains microbial community stability

The ISME Journal ◽

10.1038/ismej.2013.108 ◽

2013 ◽

Vol 7 (11) ◽

pp. 2126-2136 ◽

Cited By ~ 93

Author(s):

Oylum Erkus ◽

Victor CL de Jager ◽

Maciej Spus ◽

Ingrid J van Alen-Boerrigter ◽

Irma MH van Rijswijck ◽

...

Keyword(s):

Microbial Community ◽

Community Stability

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In-well sediment incubators to evaluate microbial community stability and dynamics following bioimmobilization of uranium

Remediation Journal ◽

10.1002/rem.20218 ◽

2009 ◽

Vol 19 (4) ◽

pp. 73-89

Author(s):

Brett R. Baldwin ◽

Aaron D. Peacock ◽

Ying-Dong Margaret Gan ◽

C. Tom Resch ◽

Evan Arntzen ◽

...

Keyword(s):

Microbial Community ◽

Community Stability

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

10.5194/egusphere-egu21-8920 ◽

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&#8211;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 &#181;m 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>

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Effect of prophylactic dextrose gel on the neonatal gut microbiome

Archives of Disease in Childhood - Fetal and Neonatal Edition ◽

10.1136/archdischild-2021-322757 ◽

2021 ◽

pp. fetalneonatal-2021-322757

Author(s):

Sophie L St Clair ◽

Jane E Harding ◽

Justin M O’Sullivan ◽

Gregory D Gamble ◽

Jane M Alsweiler ◽

...

Keyword(s):

Microbial Community ◽

Relative Abundance ◽

Gut Microbiome ◽

Beta Diversity ◽

Alpha Diversity ◽

Community Stability ◽

Neonatal Hypoglycaemia ◽

Bacterial Dna ◽

Dna Concentration ◽

Stool Samples

ObjectiveTo determine the effect of prophylactic dextrose gel on the infant gut microbiome.DesignObservational cohort study nested in a randomised trial.SettingThree maternity hospitals in New Zealand.PatientsInfants at risk of neonatal hypoglycaemia whose parents consented to participation in the hypoglycaemia Prevention in newborns with Oral Dextrose trial (hPOD). Infants were randomised to receive prophylactic dextrose gel or placebo gel, or were not randomised and received no gel (controls). Stool samples were collected on days 1, 7 and 28.Main outcome measuresThe primary outcome was microbiome beta-diversity at 4 weeks. Secondary outcomes were beta-diversity, alpha-diversity, bacterial DNA concentration, microbial community stability and relative abundance of individual bacterial taxa at each time point.ResultsWe analysed 434 stool samples from 165 infants using 16S rRNA gene amplicon sequencing. There were no differences between groups in beta-diversity at 4 weeks (p=0.49). There were also no differences between groups in any other microbiome measures including beta-diversity (p=0.53 at day 7), alpha-diversity (p=0.46 for day 7 and week 4), bacterial DNA concentration (p=0.91), microbial community stability (p=0.52) and microbial relative abundance at genus level. There was no evidence that exposure to any dextrose gel (prophylaxis or treatment) had any effect on the microbiome. Mode of birth, type of milk fed, hospital of birth and ethnicity were all associated with differences in the neonatal microbiome.ConclusionsClinicians and consumers can be reassured that dextrose gel used for prophylaxis or treatment of neonatal hypoglycaemia does not alter the neonatal gut microbiome.Trial registration number12614001263684.

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