Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake ...brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.
We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L
. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.
Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.
•Review of aquatic RNA viromics and metatranscriptomics.•Synthesis and analysis of the results of these studies.•Perspective on the future directions of the field of research.
RNA viruses that infect ...microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generated unprecedented insight into this relatively understudied class of microbes. Here, the relevant literature is summarized and discussed, including viromic studies of extracellular aquatic RNA viral assemblages, and transcriptomic studies of active and associated RNA viruses from aquatic environments followed by commentary on the present challenges and future directions of this field of research.
ABSTRACT
Geographic patterns of bacteria and microeukaryotes have attracted increasing attention. However, mechanisms underlying geographic patterns in the community composition of both microbial ...groups are still poorly resolved. In particular, knowledge of whether bacterial communities and microeukaryotic communities are subject to the same or different assembly mechanisms is still limited. In this study, we investigated the biogeographic patterns of bacterial and microeukaryotic communities of 23 lakes on the Tibetan Plateau and quantified the relative influence of assembly mechanisms in shaping both microbial communities. Results showed that water salinity was the major driving force in controlling the community structures of bacteria and microeukaryotes. Although bacterial and microeukaryotic communities exhibited similar distance-decay patterns, the bacterial communities were mainly governed by environmental filtering (a niche-related process), whereas microeukaryotic communities were strongly driven by dispersal limitation (a neutral-related process). Furthermore, we found that bacteria exhibited wider niche breadths and higher dispersal ability but lower community stabilities than microeukaryotes. The similar distribution patterns but contrasting assembly mechanisms effecting bacteria and microeukaryotes resulted from the differences in dispersal ability and community stability. Our results highlight the importance of considering organism types in studies of the assembly mechanisms that shape microbial communities in microbial ecology.
This study demonstrates that bacterial communities are mainly governed by environmental filtering whereas microeukaryotic communities are more strongly driven by dispersal limitation in Tibetan lakes.
Abstract Members of the phylum Gemmatimonadota can account for up to 10% of the phylogenetic diversity in bacterial communities. However, a detailed investigation of their cell biology and ecological ...roles is restricted by currently only six characterized species. By combining low-nutrient media, empirically determined inoculation volumes and long incubation times in a 96-well plate cultivation platform, we isolated two strains from a limnic sponge that belong to this under-studied phylum. The characterization suggests that the two closely related strains constitute a novel species of a novel genus, for which we introduce the name Pseudogemmatithrix spongiicola . The here demonstrated isolation of novel members from an under-studied bacterial phylum substantiates that the cultivation platform can provide access to axenic bacterial cultures from various environmental samples. Similar to previously described members of the phylum, the novel isolates form spherical appendages at the cell poles that were believed to be daughter cells resulting from asymmetric cell division by budding. However, time-lapse microscopy experiments and quantitative image analysis showed that the spherical appendages never grew or divided. Although the role of these spherical cells remains enigmatic, our data suggests that cells of the phylum Gemmatimonadota divide via FtsZ-based binary fission with different division plane localization patterns than in other bacterial phyla.
The bacterial phylum Verrucomicrobia was formally described two decades ago and originally believed to be a minor member of many ecosystems; however, it is now recognized as ubiquitous and abundant ...in both soil and aquatic systems. Nevertheless, knowledge of the drivers of its relative abundance and within-phylum habitat preferences remains sparse, especially in lake systems. Here, we documented the distribution of Verrucomicrobia in 12 inland lakes in Southeastern Michigan, a Laurentian Great Lake (Lake Michigan), and a freshwater estuary, which span a gradient in lake sizes, depths, residence times, and trophic states. A wide range of physical and geochemical parameters was covered by sampling seasonally from the surface and bottom of each lake, and by separating samples into particle-associated and free-living fractions. On average, Verrucomicrobia was the 4th most abundant phylum (range 1.7-41.7%). Fraction, season, station, and depth explained up to 70% of the variance in Verrucomicrobia community composition and preference for these habitats was phylogenetically conserved at the class-level. When relative abundance was linearly modeled against environmental data, Verrucomicrobia and non-Verrucomicrobia bacterial community composition correlated to similar quantitative environmental parameters, although there were lake system-dependent differences and > 55% of the variance remained unexplained. A majority of the phylum exhibited preference for the particle-associated fraction and two classes (Opitutae and Verrucomicrobiae) were identified to be more abundant during the spring season. This study highlights the high relative abundance of Verrucomicrobia in north temperate lake systems and expands insights into drivers of within-phylum habitat preferences of the Verrucomicrobia.
ABSTRACT
Several cyanobacteria, including diazotrophic Raphidiopsis raciborskii, can form harmful blooms when dissolved inorganic phosphorus concentrations are very low. We hypothesized that R. ...raciborskii strains would vary in phosphorus (P) allocations to cell growth and storage, providing resilience of populations to continuously low or variable P supplies. We tested this hypothesis using six toxic strains (producing cylindrospermopsins) isolated from a field population using batch monocultures with and without P and dissolved inorganic nitrogen (DIN). Treatments replete with DIN, irrespective of P addition, had similar exponential growth rates for individual strains. P storage capacity varied 4-fold among strains and was significantly higher in DIN-free treatments than in replete treatments. P was stored by all R. raciborskii strains, in preference to allocation to increase growth rates. P stores decreased with increased growth rate across strains, but weeere not related to the time to P starvation in P-free treatments. The storage capacity of R. raciborskii, combined with strategies to efficiently uptake P, means that P controls may not control R. raciborskii populations in the short term. Intra-population strain variation in P storage capacity will need to be reflected in process-based models to predict blooms of R. raciborskii and other cyanobacteria adapted to low-P conditions.
Strains of the cyanobacterial speciesRaphidiopsis raciborskii preferentially stored phosphorus over growth allocation to confer a longer growth period and support population persistence.
Floating life (obligate neuston) is a core component of the ocean surface food web. However, only 1 region of high neustonic abundance is known so far, the Sargasso Sea in the Subtropical North ...Atlantic gyre, where floating life provides critical habitat structure and ecosystem services. Here, we hypothesize that floating life is also concentrated in other gyres with converging surface currents. To test this hypothesis, we collected samples through the eastern North Pacific Subtropical Gyre in the area of the North Pacific "Garbage Patch" (NPGP) known to accumulate floating anthropogenic debris. We found that densities of floating life were higher inside the central NPGP than on its periphery and that there was a positive relationship between neuston abundance and plastic abundance for 3 out of 5 neuston taxa, Velella, Porpita, and Janthina. This work has implications for the ecology of subtropical oceanic gyre ecosystems.
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