Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats

Chiang, Edna; Schmidt, Marian L.; Berry, Michelle A.; Biddanda, Bopaiah A.; Burtner, Ashley M.; Johengen, Thomas H.; Palladino, Danna; Denef, Vincent J.

doi:10.1371/journal.pone.0195112

Cited by 56 publications

(39 citation statements)

References 64 publications

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“…Interestingly, we noticed a significant proportion of sequences assigned to members of the phylum Verrucomicrobia, in particular in water samples (∼8%, Supplementary Datasheet 1 ). This observation is congruent with the ubiquity ( Zwart et al, 2003 ) and dominance ( Chiang et al, 2018 ) of this phylum in lake habitats. Together these data suggest that, if any bias was introduced during the nested-PCR approach, this bias had a limited impact on the composition of the tested microbial communities.…”

Section: Resultssupporting

confidence: 84%

Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia

et al. 2018

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Phragmites australis and Typha latifolia are two macrophytes commonly present in natural and artificial wetlands. Roots of these plants engage in interactions with a broad range of microorganisms, collectively referred to as the microbiota. The microbiota contributes to the natural process of phytodepuration, whereby pollutants are removed from contaminated water bodies through plants. The outermost layer of the root corpus, the rhizoplane, is a hot-spot for these interactions where microorganisms establish specialized aggregates designated biofilm. Earlier studies suggest that biofilm-forming members of the microbiota play a crucial role in the process of phytodepuration. However, the composition and recruitment cue of the Phragmites, and Typha microbiota remain poorly understood. We therefore decided to investigate the composition and functional capacities of the bacterial microbiota thriving at the P. australis and T. latifolia root–soil interface. By using 16S rRNA gene Illumina MiSeq sequencing approach we demonstrated that, despite a different composition of the initial basin inoculum, the microbiota associated with the rhizosphere and rhizoplane of P. australis and T. latifolia tends to converge toward a common taxonomic composition dominated by members of the phyla Actinobacteria, Firmicutes, Proteobacteria, and Planctomycetes. This indicates the existence of a selecting process acting at the root–soil interface of these aquatic plants reminiscent of the one observed for land plants. The magnitude of this selection process is maximum at the level of the rhizoplane, where we identified different bacteria enriched in and discriminating between rhizoplane and rhizosphere fractions in a species-dependent and -independent way. This led us to hypothesize that the structural diversification of the rhizoplane community underpins specific metabolic capabilities of the microbiota. We tested this hypothesis by complementing the sequencing survey with a biochemical approach and scanning electron microscopy demonstrating that rhizoplane-enriched bacteria have a bias for biofilm-forming members. Together, our data will be critical to facilitate the rational exploitation of plant–microbiota interactions for phytodepuration.

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Section: Resultssupporting

confidence: 84%

Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia

et al. 2018

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“…In Pamvotis lake in winter, Actinobacteria dropped to <10% and instead, Verrucomicrobia occurred in relative abundance >30%. These data support recent findings that Verrucomicrobia may constitute a high fraction of the bacterial communities [49]. The phylum has been associated with phytoplankton blooms and/or specific complex substrates [50,51] and single cell genomics have revealed genes for enzymes degrading a wide spectrum of polysaccharides by its representatives [52].…”

Section: Discussionsupporting

confidence: 88%

Diversity of Bacteria in Lakes with Different Chlorophyll Content and Investigation of Their Respiratory Activity through a Long-Term Microcosm Experiment

Karayanni

Macingo

Tolis

et al. 2019

Water

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Bacterial community structure and metabolism are critical factors for ecosystem functioning since they affect remineralization of nutrients and carbon flow. We used Illumina sequencing of 16SrRNA V3-V4 regions to investigate whether bacterial assemblage composition differs between four samples from two lakes in the geographic region of Epirus (Greece) characterized by distinct oligotrophic to eutrophic/hypereutrophic conditions as revealed by chlorophyll-a values. We found high similarity (>60%) for bacterial assemblages recovered from the two lakes when eutrophic/hypereutrophic conditions prevailed. Distinct bacterial communities appeared in oligotrophic and mesotrophic waters. Low temperature was occasionally an important factor in shaping the bacterial community. In parallel, microcosm experiments were performed to estimate respiration rates of bacterioplankton at in situ temperature and under a 2 °C temperature increase scenario. Differently assembled communities were found to display similar rates except under hypereutrophic conditions when respiration increased significantly, leading to hypoxic conditions. Temperature increase did not affect respiration rates. Overall this study indicated a clear differentiation of bacterial communities between sites of different trophic state. However, different communities responded similarly under a specific range of chlorophyll-a values and resisted small scale temperature perturbations. Different results were found for hypereutrophic conditions and this has implications for ecosystems functioning, given the increasing occurrence of eutrophication events.

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“…While the concept that dolomite forms within sediments mediated by anaerobic microbial processes and their extracellular polymeric substances is widely acknowledged, another aspect should be taken into account: the site of dolomite formation may not always coincide with the location where the mineral is found due to relocation after precipitation. Several studies describe unlithified dolomite precipitation in warm, arid and hypersaline marine environments, like coastal sabkhas (Illing et al, 1965;Bontognali et al, 2010;Court et al, 2017), coastal lakes, such as Lagoa Vermelha in Brazil (Vasconcelos and McKenzie, 1997;van Lith et al, 2002;Sánchez-Román et al, 2009), and ephemeral lakes along the Coorong lagoon in southern Australia (von der Borch, 1976;Rosen et al, 1989;Warren, 1990;Wright and Wacey, 2005). Dolomite precipitation is further reported in endorheic hypersaline lakes, e.g., Qinghai Lake in Tibet (Deng et al, 2010), Lake Acıgöl (Turkey;Balci et al, 2016) and alkaline playa lakes such as Deep Springs Lake in California (Meister et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Authigenic formation of Ca–Mg carbonates in the shallow alkaline Lake Neusiedl, Austria

Fussmann¹,

Hoyningen-Huene²,

Reimer³

et al. 2020

Biogeosciences

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Abstract. Despite advances regarding the microbial and organic-molecular impact on nucleation, the formation of dolomite in sedimentary environments is still incompletely understood. Since 1960, apparent dolomite formation has been reported from mud sediments of the shallow, oligohaline and alkaline Lake Neusiedl, Austria. To trace potential dolomite formation or diagenetic alteration processes in its deposits, lake water samples and sediment cores were analyzed with respect to sediment composition, hydrochemistry and bacterial community composition. Sediments comprise 20 cm of homogenous mud with 60 wt % carbonate, which overlies dark-laminated consolidated mud containing 50 wt % carbonate and plant debris. Hydrochemical measurements reveal a shift from oxic lake water with pH 9.0 to anoxic sediment pore water with pH 7.5. A decrease in SO42- with a concomitant increase in ΣH2S and NH4+ from 0 to 15 cm core depth indicates anaerobic heterotrophic decomposition, including sulfate reduction. The bacterial community composition reflects the zonation indicated by the pore water chemistry, with a distinct increase in fermentative taxa below 15 cm core depth. The water column is highly supersaturated with respect to (disordered) dolomite and calcite, whereas saturation indices of both minerals rapidly approach zero in the sediment. Notably, the relative proportions of different authigenic carbonate phases and their stoichiometric compositions remain constant with increasing core depth. Hence, evidence for Ca–Mg carbonate formation or ripening to dolomite is lacking within the sediment of Lake Neusiedl. As a consequence, precipitation of high-magnesium calcite (HMC) and protodolomite does not occur in association with anoxic sediment and sulfate-reducing conditions. Instead, analytical data for Lake Neusiedl suggest that authigenic HMC and protodolomite precipitate from the supersaturated, well-mixed aerobic water column. This observation supports an alternative concept to dolomite formation in anoxic sediments, comprising Ca–Mg carbonate precipitation in the water column under aerobic and alkaline conditions.

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Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats

Cited by 56 publications

References 64 publications

Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia

Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia

Diversity of Bacteria in Lakes with Different Chlorophyll Content and Investigation of Their Respiratory Activity through a Long-Term Microcosm Experiment

Authigenic formation of Ca–Mg carbonates in the shallow alkaline Lake Neusiedl, Austria

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