Virioplankton Community Structure in Tunisian Solar Salterns

ABSTRACTThe microbial community inhabiting Sfax solar salterns on the east coast of Tunisia has been studied by means of different molecular and culture-dependent tools that have unveiled the presence of novel microbial groups as well as a community structure different from that of other coastal hypersaline environments. We have focused on the study of the viral assemblages of these salterns and their changes along the salinity gradient and over time. Viruses from three ponds (C4, M1, and TS) encompassing salinities from moderately hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in May and October 2009 and analyzed by transmission electron microscopy (TEM) and pulsed-field gel electrophoresis (PFGE). Additionally, for all three October samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios, increased along the salinity gradient, with around 1010virus-like particles (VLPs)/ml in close-to-saturation ponds, which represents the highest viral concentration reported so far for aquatic systems. Four distinct morphologies could be observed with TEM (spherical, tailed, spindled, and filamentous) but with various proportions in the different samples. Metagenomic analyses indicated that every pond harbored a distinct viral assemblage whose G+C content could be roughly correlated with that of the active part of the microbial community that may have constituted the putative hosts. As previously reported for hypersaline metaviromes, most sequences did not have matches in the databases, although some were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide frequency analyses indicated that (i) factors additional to salinity could be structuring viral communities and (ii) every metavirome had unique gene contents and dinucleotide frequencies. Comparison with hypersaline metaviromes available in the databases indicated that the viral assemblages present in close-to-saturation environments located thousands of kilometers apart presented some common traits among them in spite of their differences regarding the putative hosts. A small core metavirome for close-to-saturation systems was found that contained 7 sequences of around 100 nucleotides (nt) whose function was not hinted at byin silicosearch results, although it most likely represents properties essential for hyperhalophilic viruses.

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The influence of light on soil community structure and consequences for soil CO2, CO18O and COS exchange

10.5194/egusphere-egu2020-20422 ◽

2020 ◽

Author(s):

Lisa Wingate ◽

Clement Foucault ◽

Nicolas Fanin ◽

Joana Sauze ◽

Pierre-Alain Maron ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Soil Ph ◽

Isotope Composition ◽

Light Availability ◽

Alkaline Soils ◽

Soil Microbial ◽

Microbial Groups ◽

Taxonomic Groups ◽

Carbonyl Sulphide

The stable oxygen isotope composition of atmospheric CO2 and the mixing ratio of carbonyl sulphide (COS) are potential tracers of biospheric CO2 fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (&#945;, &#946; and &#947;) may have different affinities to CO2 and COS and their expression should also vary between different microbial groups, differences in the community structure could impact the &#8216;community-integrated&#8217; CA activity differently for CO2 and COS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO2, CO18O and COS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototroph genes. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO2 sink and the CA-driven CO2-H2O isotopic exchange rates correlated with phototroph abundance. COS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. In addition we developed a metabarcoding approach to reveal the interactions of specific taxonomic groups incuding photosynthetic eukaryotic algae and cyanobacteria when exposed to light and their impact on flux rates. Our findings demonstrate that soil-atmosphere CO2, COS and CO18O fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and support the idea that different members of the microbial community express different classes of CA, with different affinities to CO2 and COS.

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Soil viral communities are structured by pH at local and global scales

10.1101/2021.10.20.465127 ◽

2021 ◽

Author(s):

Sungeun Lee ◽

Jackson W Sorensen ◽

Robin L Walker ◽

Joanne B Emerson ◽

Graeme W Nicol ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Soil Ph ◽

Environmental Gradients ◽

Abiotic Factors ◽

Global Scale ◽

Community Structures ◽

Viral Community ◽

Viral Communities ◽

Virus Communities

Viruses shape microbial community structures, impacting metabolic pathways and influencing biogeochemical cycles. Despite their importance, the influence of biotic and abiotic factors on viral community structures across environmental gradients in soil is relatively unknown compared to their prokaryotic hosts. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil virus communities. In this study, prokaryotic and viral communities were characterized in soils sampled from the extremes of a long-term pH-manipulated soil gradient (pH 4.5 and 7.5), and viral populations were compared to those in a variety of soil ecosystems ranging in pH (4.0 - 7.5). Prokaryotic and viral community structure were significantly influenced by soil pH at the local scale. Of 1,910 viral operational taxonomic units (vOTUs), 99% were restricted to pH 4.5 or 7.5 soil only. These were compared in gene sharing networks of populations from six other European and North American soil systems. A selection of viral clusters from acidic and neutral pH soils were more associated with those from the local gradient pH 4.5 or 7.5 soils, respectively. Results indicate that as with prokaryotes, soil pH is a factor structuring viral communities at the local and global scale.

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Polar lipids and pigments as biomarkers for the study of the microbial community structure of solar salterns

Saline Lakes ◽

10.1007/978-94-017-2934-5_8 ◽

2001 ◽

pp. 81-89

Author(s):

Carol D. Litchfield ◽

Aharon Oren

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Polar Lipids ◽

Solar Salterns

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Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems

mSystems ◽

10.1128/msystems.00098-20 ◽

2020 ◽

Vol 5 (2) ◽

Cited By ~ 1

Author(s):

R. E. Danczak ◽

R. A. Daly ◽

M. A. Borton ◽

J. C. Stegen ◽

S. Roux ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Community Assembly ◽

Trophic Levels ◽

Deep Subsurface ◽

Ecological Dynamics ◽

Selective Pressures ◽

Viral Community ◽

Viral Communities

ABSTRACT The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels. IMPORTANCE Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels.

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Influence of Estuarine Water on the Microbial Community Structure of Patagonian Fjords

Frontiers in Marine Science ◽

10.3389/fmars.2021.611981 ◽

2021 ◽

Vol 8 ◽

Author(s):

Javier Tamayo-Leiva ◽

Jerónimo Cifuentes-Anticevic ◽

Pilar Aparicio-Rizzo ◽

José Ignacio Arroyo ◽

Italo Masotti ◽

...

Keyword(s):

Climate Change ◽

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Linear Span ◽

Salinity Gradient ◽

Estuarine Water ◽

Eukaryotic Phytoplankton ◽

Patagonian Fjords ◽

Sar11 Clade

Fjords are sensitive areas affected by climate change and can act as a natural laboratory to study microbial ecological processes. The Chilean Patagonian fjords (41–56°S), belonging to the Subantarctic ecosystem (46–60°S), make up one of the world’s largest fjord systems. In this region, Estuarine Water (EW) strongly influences oceanographic conditions, generating sharp gradients of oxygen, salinity and nutrients, the effects of which on the microbial community structure are poorly understood. During the spring of 2017 we studied the ecological patterns (dispersal and oceanographic factors) underlying the microbial community distribution in a linear span of 450 km along the estuarine-influenced Chilean Patagonian fjords. Our results show that widespread microbial dispersion existed along the fjords where bacterioplankton exhibited dependence on the eukaryotic phytoplankton community composition. This dependence was particularly observed under the low chlorophyll-a conditions of the Baker Channel area, in which a significant relationship was revealed between SAR11 Clade III and the eukaryotic families Pyrenomonadaceae (Cryptophyte) and Coccomyxaceae (Chlorophyta). Furthermore, dissolved oxygen and salinity were revealed as the main drivers influencing the surface marine microbial communities in these fjords. A strong salinity gradient resulted in the segregation of the Baker Channel prokaryotic communities from the rest of the Patagonian fjords. Likewise, Microbacteriaceae, Burkholderiaceae and SAR11 Clade III, commonly found in freshwater, were strongly associated with EW conditions in these fjords. The direct effect of EW on the microbial community structure and diversity of the fjords exemplifies the significance that climate change and, in particular, deglaciation have on this marine region and its productivity.

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The natural recovery of soil microbial community and nitrogen functions after pasture abandonment in the Amazon region

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa149 ◽

2020 ◽

Vol 96 (9) ◽

Cited By ~ 1

Author(s):

Alexandre Pedrinho ◽

Lucas William Mendes ◽

Luis Fernando Merloti ◽

Fernando Dini Andreote ◽

Siu Mui Tsai

Keyword(s):

Community Structure ◽

Microbial Community ◽

Secondary Forest ◽

Soil Microbial Communities ◽

Forest Growth ◽

Potential Functions ◽

Soil Microbial ◽

Microbial Groups ◽

Forest To Pasture Conversion ◽

Pasture Conversion

ABSTRACT We assessed the impacts of forest-to-pasture conversion on the dynamic of soil microbial communities, especially those involved in the N-cycle, and their potential functions, using DNA-metagenomic sequencing coupled with the quantification of marker genes for N-cycling. We also evaluated whether the community's dynamic was reestablished with secondary forest growth. In general, the microbial community structure was influenced by changes in soil chemical properties. Aluminum and nitrate significantly correlated to community structure and with 12 out of 21 microbial phyla. The N-related microbial groups and their potential functions were also affected by land-use change, with pasture being clearly different from primary and secondary forest systems. The microbial community analysis demonstrated that forest-to-pasture conversion increased the abundance of different microbial groups related to nitrogen fixation, including Bacteroidetes, Chloroflexi and Firmicutes. In contrast, after pasture abandonment and with the secondary forest regeneration, there was an increase in the abundance of Proteobacteria taxa and denitrification genes. Our multi-analytical approach indicated that the secondary forest presented some signs of resilience, suggesting that the N-related microbial groups and their potential functions can be recovered over time with implications for future ecological restoration programs.

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