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

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.

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

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
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.

scholarly journals High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

2020 ◽  
Author(s):  
Wu Qu ◽  
Boliang Gao ◽  
Jie Wu ◽  
Min Jin ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Amplicon Sequencing ◽  
Biotic Factors ◽  
Community Structures ◽  
Mangrove Sediments ◽  
Element Cycling ◽  
Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

scholarly journals Variations in microbial community structure and functional gene expression in bio-treatment processes with odorous pollutants

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weidong Li ◽  
Jianguo Ni ◽  
Shaoqin Cai ◽  
Ying Liu ◽  
Chenjia Shen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Community Structures ◽  
Industrial Emissions ◽  
Gas Treatment ◽  
Kegg Pathways ◽  
Microbial Community Structures

AbstractEngineered microbial ecosystems in biofilters have been widely applied to treat odorous gases from industrial emissions. Variations in microbial community structure and function associated with the removal of odorous gases by biofilters are largely unknown. This study performed a metagenomic analysis to discover shifts in microbial community structures in a commercial scale biofilter after treating odorous gas. Our study identified 175,675 functional genes assigned into 43 functional KEGG pathways. Based on the unigene sequences, there were significant changes in microbial community structures in the biofilter after treating odorous gas. The dominant genera were Thiobacillus and Oceanicaulis before the treatment, and were Acidithiobacillus and Ferroplasma after the treatment. A clustering analysis showed that the number of down-regulated microbes exceeded the number of up-regulated microbes, suggesting that odorous gas treatment reduced in microbial community structures. A differential expression analysis identified 29,975 up- and 452,599 down-regulated genes. An enrichment analysis showed 17 classic types of xenobiotic biodegradation pathways. The results identified 16 and 15 genes involved in ammonia and sulfite metabolism, respectively; an analysis of their relative abundance identified several up-regulated genes, which may be efficient genes involved in removing odorous gases. The data provided in this study demonstrate the changes in microbial communities and help identify the dominant microflora and genes that play key roles in treating odorous gases.

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

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

<p>The stable oxygen isotope composition of atmospheric CO<sub>2</sub> and the mixing ratio of carbonyl sulphide (COS) are potential tracers of biospheric CO<sub>2</sub> 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 (α, β and γ) may have different affinities to CO<sub>2</sub> and COS and their expression should also vary between different microbial groups, differences in the community structure could impact the ‘community-integrated’ CA activity differently for CO<sub>2</sub> 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 CO<sub>2</sub>, CO<sup>18</sup>O 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 CO<sub>2</sub> sink and the CA-driven CO<sub>2</sub>-H<sub>2</sub>O 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 CO<sub>2</sub>, COS and CO<sup>18</sup>O 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 CO<sub>2</sub> and COS.</p>

scholarly journals Virioplankton Community Structure in Tunisian Solar Salterns

2012 ◽  
Vol 78 (20) ◽  
pp. 7429-7437 ◽  
Author(s):  
Ines Boujelben ◽  
Pablo Yarza ◽  
Cristina Almansa ◽  
Judith Villamor ◽  
Sami Maalej ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Salinity Gradient ◽  
Hypersaline Environments ◽  
Metagenomic Dna ◽  
Solar Salterns ◽  
Transmission Electron ◽  
Viral Communities ◽  
Microbial Groups ◽  
Saturation Systems

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.

Formation and succession of microbial community structure in different ecological niches under reclaimed water acclimation

2020 ◽  
Author(s):  
Jie Li ◽  
Yujiao Sun ◽  
Xiaoyu Wang ◽  
Meng Yin ◽  
Shangwei Xu
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Water Resources ◽  
Natural Water ◽  
Reclaimed Water ◽  
Ecological Niches ◽  
Community Structures ◽  
Significant Difference ◽  
Microbial Community Structures ◽  
The Difference

<p>Using reclaimed water as a resource for landscape water replenishment may alleviate the major problems of water resource shortages and water environment pollution. However, the safety of the water and the risk of eutrophication remain doubted by the public. Our study aimed to reveal the difference between natural water and reclaimed water and to discuss the rationality of reclaimed water replenishment from the perspective of microorganisms. We analyzed the microbial community structures in natural water, reclaimed water and natural biofilms and the community succession was clarified along the ecological niches, water resources, liquidity and time using 16S rRNA gene amplicon sequencing. Primary biofilms without the original community were added to study the formation of microbial community structures under reclaimed water acclimation. The results showed that the difference caused by ecological niches was more than those caused by the liquidity of water and different water resources. No significant difference was found in the microbial diversity and community structure caused by the addition of reclaimed water. Based on the microbial analysis, reclaimed water replenishment is a feasible solution that can be used for supplying river water. Innovatively, we introduced the study of biofilms and determined that the monitoring of biofilms or sediments closely related to water was also important for the early warning of water bloom, providing a unique perspective for the management of eutrophication.</p>

scholarly journals Biome-Level Biogeography of Streambed Microbiota

2008 ◽  
Vol 74 (10) ◽  
pp. 3014-3021 ◽  
Author(s):  
Robert H. Findlay ◽  
Christine Yeates ◽  
Meredith A. J. Hullar ◽  
David A. Stahl ◽  
Louis A. Kaplan
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Bacterial Community ◽  
Microbial Community Structure ◽  
Bacterial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Principal Component ◽  
Community Structures ◽  
Microbial Community Structures

ABSTRACT A field study was conducted to determine the microbial community structures of streambed sediments across diverse geographic and climatic areas. Sediment samples were collected from three adjacent headwater forest streams within three biomes, eastern deciduous (Pennsylvania), southeastern coniferous (New Jersey), and tropical evergreen (Guanacaste, Costa Rica), to assess whether there is biome control of stream microbial community structure. Bacterial abundance, microbial biomass, and bacterial and microbial community structures were determined using classical, biochemical, and molecular methods. Microbial biomass, determined using phospholipid phosphate, was significantly greater in the southeastern coniferous biome, likely due to the smaller grain size, higher organic content, and lower levels of physical disturbance of these sediments. Microbial community structure was determined using phospholipid fatty acid (PLFA) profiles and bacterial community structure from terminal restriction fragment length polymorphism and edited (microeukaryotic PLFAs removed) PLFA profiles. Principal component analysis (PCA) was used to investigate patterns in total microbial community structure. The first principal component separated streams based on the importance of phototrophic microeukaryotes within the community, while the second separated southeastern coniferous streams from all others based on increased abundance of fungal PLFAs. PCA also indicated that within- and among-stream variations were small for tropical evergreen streams and large for southeastern coniferous streams. A similar analysis of bacterial community structure indicated that streams within biomes had similar community structures, while each biome possessed a unique streambed community, indicating strong within-biome control of stream bacterial community structure.

scholarly journals Liming Alters the Soil Microbial Community and Extracellular Enzymatic Activities in Temperate Coniferous Forests

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 190
Author(s):  
Sangsub Cha ◽  
Yong Suk Kim ◽  
Ah Lim Lee ◽  
Dong-Hyeon Lee ◽  
Namin Koo
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Bacterial Community ◽  
Soil Ph ◽  
Fungal Community ◽  
Anthropogenic Activities ◽  
Soil Microbial Communities ◽  
Lime Treatment ◽  
Soil Microbial

Soil acidification caused by anthropogenic activities adversely affects forest ecosystems by altering soil pH, which is an important factor in soil quality and function. Liming is one suggested way to solve this problem. This study was performed to evaluate the effects of liming in acidic forest soils by determining soil microbial biomass, microbial community structure, and extracellular enzyme activities associated with carbon, nitrogen, and phosphorus cycling. Lime treatment increased soil pH by up to 40%, significantly increased organic matter (OM) content at some sites, and altered the enzyme activity of the soil. With liming, the microbial biomass appeared to be affected by the chemical properties of the soil, such as pH, Ca2+, Mg2+, K+, and exchangeable aluminum (Ale) levels, although there were no significant differences at the site level. Enzymatic activity was found to be affected by pH, Ca2+, Mg2+, electrical conductivity (EC), and Ale; and acid phosphatase (AP) and phenol oxidase (POX) activity were significantly affected by lime treatment. AP activity decreased from 0.62 to 0.66, and POX activity increased from 1.75 to 3.00 in part of the sites. The bacterial community richness was influenced by pH as a direct effect of lime treatment. The fungal community richness was associated with changes in K+ that were not due to lime treatment. The bacterial community structure was affected by soil OM, total nitrogen (TN), pH, and Ca2+; and the fungal community structure was affected by pH, Mg2+, and K+. In conclusion, changes in soil environmental conditions by liming can affect soil microbial communities and functions through direct or indirect processes, further changing ecosystem processes.

scholarly journals The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water

2021 ◽  
Vol 12 ◽  
Author(s):  
Chiqian Zhang ◽  
Ke Qin ◽  
Ian Struewing ◽  
Helen Buse ◽  
Jorge Santo Domingo ◽  
...  
Keyword(s):  
Water Quality ◽  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Water Temperature ◽  
Water Samples ◽  
Tap Water ◽  
Community Diversity ◽  
Community Structures ◽  
Bacterial Community Diversity

Microbial drinking water quality in premise plumbing systems (PPSs) strongly affects public health. Bacterial community structure is the essential aspect of microbial water quality. Studies have elucidated the microbial community structure in cold tap water, while the microbial community structures in hot tap and shower water are poorly understood. We sampled cold tap, hot tap, and shower water from a simulated PPS monthly for 16 consecutive months and assessed the bacterial community structures in those samples via high-throughput sequencing of bacterial 16S rRNA genes. The total relative abundance of the top five most abundant phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes) was greater than 90% among the 24 identified phyla. The most abundant families were Burkholderiaceae, Sphingomonadaceae, unclassified Alphaproteobacteria, unclassified Corynebacteriales, and Mycobacteriaceae. A multiple linear regression suggests that the bacterial community diversity increased with water temperature and the age of the simulated PPS, decreased with total chlorine residual concentration, and had a limited seasonal variation. The bacterial community in hot tap water had significantly lower Shannon and Inverse Simpson diversity indices (p < 0.05) and thus a much lower diversity than those in cold tap and shower water. The paradoxical results (i.e., diversity increased with water temperature, but hot tap water bacterial community was less diverse) were presumably because (1) other environmental factors made hot tap water bacterial community less diverse, (2) the diversity of bacterial communities in all types of water samples increased with water temperature, and (3) the first draw samples of hot tap water could have a comparable or even lower temperature than shower water samples and the second draw samples of cold tap water. In both a three-dimensional Non-metric multidimensional scaling ordination plot and a phylogenetic dendrogram, the samples of cold tap and shower water cluster and are separate from hot tap water samples (p < 0.05). In summary, the bacterial community in hot tap water in the simulated PPS had a distinct structure from and a much lower diversity than those in cold tap and shower water.

scholarly journals Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System, Manatee Springs, Florida

2021 ◽  
Author(s):  
Kema Malki ◽  
Natalie A. Sawaya ◽  
Michael J. Tisza ◽  
Felipe H. Coutinho ◽  
Karyna Rosario ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Spatiotemporal Variability ◽  
Drinking Water Source ◽  
Aquifer System ◽  
Floridan Aquifer ◽  
Viral Community ◽  
Suwannee River ◽  
Viral Communities

Flow from high magnitude springs fed by the Floridan aquifer system contribute hundreds of liters of water per second to rivers, creating unique lotic systems. Despite their importance as freshwater sources and their contributions to the state’s major rivers, little is known about the composition and spatiotemporal variability of prokaryotic and viral communities of these spring systems or their influence on downstream river sites. At four time points throughout a year, we determined the abundance and diversity of prokaryotic and viral communities at three sites within the first-magnitude Manatee Springs system (the spring head where water emerges from the aquifer, a mixed region where the spring run ends, and a downstream site in the Suwannee River). The abundance of prokaryotes and virus-like particles increased 100-fold from the spring head to the river and few members from the head communities persisted in the river at low abundance, suggesting the springs play a minor role in seeding downstream communities. Prokaryotic and viral communities within Manatee Springs clustered by site, with seasonal variability likely driven by flow. As water flowed through the system, microbial community composition was affected by changes in physiochemical parameters and community coalescence. Evidence of species sorting and mass effects could be seen in the assemblages. Greater temporal fluctuations were observed in prokaryotic and viral community composition with increasing distance from the spring outflow, reflecting the relative stability of the groundwater environment, and comparisons to springs from prior work reaffirmed that distinct first magnitude springs support unique communities. Importance Prokaryotic and viral communities are central to food webs and biogeochemical processes in aquatic environments, where they help maintain ecosystem health. The Floridan aquifer system (FAS), which is the primary drinking water source for millions of people in the southeastern United States, contributes large amounts of freshwater to major river systems in Florida through its springs. However, there is a paucity of information regarding the spatiotemporal dynamics of microbial communities in these essential flowing freshwater systems. This work explored the prokaryotic and viral communities in a first-magnitude spring system fed by the FAS that discharges millions of liters of water per day into the Suwannee River. This study examined microbial community composition through space and time, as well as the environmental parameters and metacommunity assembly mechanisms that shape these communities, providing a foundational understanding for monitoring future changes.

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