Comparative analysis of free-living and particle-associated bacterial communities of Lake Baikal during the ice-covered period

Bashenkhaeva, Maria; Galachyants, Yuri P.; Ханаев, И. В.; Sakirko, M. V.; Petrova, Darya P.; Likhoshway, Ye. V.; Zakharova, Yulia

doi:10.1016/j.jglr.2020.03.015

Cited by 19 publications

(7 citation statements)

References 79 publications

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“…Verrucomicrobiota are ubiquitous, cosmopolitan members of freshwater microbial communities (Arnds et al, 2010; Cabello‐Yeves, Ghai, et al, 2017; Tran et al, 2018, 2021) and can be free‐living or associated with particles (Chiang et al, 2018; Parveen et al, 2013). Although usually rare, they can at times increase in abundance making up to 20% of the bacterioplankton, often in winter (Arnds et al, 2010; Bashenkhaeva et al, 2020; Cabello‐Yeves, Ghai, et al, 2017; Tran et al, 2018) and blooms of freshwater Verrucomicrobiota with relative abundance >50% of the bacterial community have been reported from Lake Baikal (Bashenkhaeva et al, 2015, 2020). Freshwater Verrucomicrobiota are taxonomically diverse (Cabello‐Yeves, Ghai, et al, 2017; 2017) with all three currently recognized Verrucomicrobiota classes (Hedlund, 2011) containing freshwater members (Figure 8D).…”

Section: Commonly Found Freshwater Microbes: the Freshwater Pelagial ...mentioning

confidence: 99%

Adaptive genetic traits in pelagic freshwater microbes

Chiriac

Haber

Salcher

2022

Environmental Microbiology

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Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free‐living, specialized oligotrophs and patch‐associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome‐assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make‐up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and ‘Ca. Patescibacteria’.

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Section: Commonly Found Freshwater Microbes: the Freshwater Pelagial ...mentioning

confidence: 99%

Adaptive genetic traits in pelagic freshwater microbes

Chiriac

Haber

Salcher

2022

Environmental Microbiology

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“…The presence of Methylacidiphilaceae in very acid samples (pH <4,7) is also in line with the extremely acidophilic nature of their unique representant, Methylacidiphilum , with optimal growth below pH 3.5 (Op den Camp et al, 2009). It is also noteworthy that this family is adapted to CH 4 and O 2 limitation (Carere et al, 2017; Smith and Wrighton, 2019) and shows a large temperature tolerance, being found from thermophilic environments (Dunfield et al, 2007; van Teeseling et al, 2014) to high latitudes (Bashenkhaeva et al, 2020; Dedysh et al, 2021; Zakharova et al, 2021).…”

Section: Resultsmentioning

confidence: 99%

Biogeography of microbial communities in high‐latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes

Seppey,

Cabrol,

Thalasso

et al. 2023

Environmental Microbiology

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Methane‐cycling is becoming more important in high‐latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high‐latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane‐cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane‐cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.

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“…For instance, several ASVs classified as Pseudorhodobacter , Candidatus Limnoluna, and Sporichthyaceae , were predicted to contribute to total enzymatic activities only during the first half of the experiment. Of these, Sporichthyaceae (Actinobacteria) has been associated with a free-living lifestyle (Bashenkhaeva et al 2020). By contrast, Cryomorphaceae (Bacteroidia) and Mycobacterium (Actinobacteria) have been associated with a particle-attached lifestyle (Delmont et al 2014, Reintjes et al 2023, Allgaier et al 2007), and from these, contribution of Mycobacterium to the community-wide predicted LAPase activity was observed only at the end of the experiment.…”

Section: Discussionmentioning

confidence: 99%

Microbial remineralization processes during post-spring-bloom excess phosphate in the northern Baltic Sea

Vanharanta,

Santoro,

Villena-Alemany

et al. 2024

Preprint

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In the northern Baltic, post-spring-bloom low dissolved inorganic nitrogen to phosphorus conditions, degradation of N-rich organic matter potentially supports the drawdown of excess phosphate. During a 17-day-long mesocosm experiment in the south-west Finnish archipelago, we examined nitrogen, phosphorus and carbon acquiring extracellular enzyme activities in three size fractions (<0.2 um, 0.2-3 um, and >3 um), bacterial abundance, production, community composition and its predicted metabolic functions. The mesocosms received different carbon and nitrogen amendments to test for the effect of inorganic nutrient stoichiometry on enzymatic degradation processes that ultimately determine the export potential of organic matter. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions. In the beginning of the experiment, peptidolytic and glycolytic enzymes were predicted to be produced by free-living bacteria identified within the classes Actinobacteria and Alphaproteobacteria, whereas the contribution of picocyanobacteria increased towards the end. Our results imply that heterotrophic bacteria lost the competition to picocyanobacteria due to the lack of suitable energy sources. The high hydrolytic rates in fractions <0.2 um and 0.2-3 um, found in this study, could potentially retain inorganic nutrients in the surface layer and suppress downward fluxes of organic matter and hence carbon sequestration.

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Comparative analysis of free-living and particle-associated bacterial communities of Lake Baikal during the ice-covered period

Cited by 19 publications

References 79 publications

Adaptive genetic traits in pelagic freshwater microbes

Adaptive genetic traits in pelagic freshwater microbes

Biogeography of microbial communities in high‐latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes

Microbial remineralization processes during post-spring-bloom excess phosphate in the northern Baltic Sea

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