Microbial Communities In Relation Research Articles

The spatiotemporal variations of microbial community in relation to water quality in a tropical drinking water reservoir, Southmost China.

It is well-known that water quality has great significance on microbial community composition in aquatic environments. In this study, we detected water column indicates the microbial community composition of nine sampling sites over two seasons using Illumina TruSeq sequencing in Songtao Reservoir, Hainan Province, Southmost China. The study indicated that the dominant phylum was Actinobacteria, Proteobacteria, Bacteroidetes, and Cyanobacteria. The diversity parameters showed that the microbial community composition had significant spatiotemporal variations, including the significantly higher Shannon index and Simpson index upstream than those midstream and downstream. Besides, there were significantly higher Chao1 index, Shannon index, and Simpson index in winter than in summer. Principal coordinates analysis (PCoA) showed the microbial structural composition had significant seasonal differences. The results of microbial community composition further revealed that the eutrophication level upstream was higher than that of midstream and downstream. The redundancy analysis (RDA) diagram indicated that the abundance of microbiology species significantly correlated with temperature, total phosphorus, Se, and Ni. Furthermore, the mantel's test showed that the temperature and total phosphorus significantly affected the community composition of archaea and bacteria. Overall, our finding here partially validated our hypothesis that the spatiotemporal variations of microbial community composition are significantly related to nutrients, physicochemical factors and metals, which has been unknown previously in tropical drinking waterbodies. This study substantially contributed to understanding of the composition of microbial community in tropical drinking water reservoirs and the main environmental driving factors in tropical zones. It also provided a reference for the management of reservoir operation to ensure drinking water safe.

Revealing soil microbial ecophysiological indicators in acidic environments laden with heavy metals via predictive modeling: Understanding the impacts of black diamond excavation

Appraising the activity of soil microbial community in relation to soil acidity and heavy metal (HM) content can help evaluate it's quality and health. Coal mining has been reported to mobilize locked HM in soil and induce acid mine drainage. In this study, agricultural soils around coal mining areas were studied and compared to baseline soils in order to comprehend the former's effect in downgrading soil quality. Acidity as well as HM fractions were significantly higher in the two contaminated zones as compared to baseline soils (p < 0.01). Moreover, self-organizing and geostatistical maps show a similar pattern of localization in metal availability and soil acidity thereby indicating a causal relationship. Sobol sensitivity, cluster, and principal component analyses were employed to enunciate the relationship between the various metal and acidity fractions with that of soil microbial properties. The results indicate a significant negative impact of metal bioavailability, and acidity on soil microbial activity. Lastly, Taylor diagrams were employed to predict soil microbial quality and health based on soil physicochemical inputs. The efficiency of several machine learning algorithms was tested to identify Random Forrest as the best model for prediction. Thus, the study imparts knowledge about soil pollution parameters, and acidity status thereby projecting soil quality which can be a pioneer in sustainable agricultural practices.

Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave.

Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.

Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites

Soil microbial communities play a key role in plant nutrition and stress tolerance. This is particularly true in sites contaminated by trace metals, which often have low fertility and stressful conditions for woody plants in particular. However, we have limited knowledge of the abiotic and biotic factors affecting the richness and composition of microbial communities inhabiting the rhizosphere of plants in contaminated sites. Using high-throughput amplicon sequencing, we studied the rhizospheric bacterial and fungal community structures of 14 woody plant families planted in three contrasting sites contaminated by metals (Pb, Cd, Zn, Mn, Fe, S). The rhizospheric bacterial communities in the given sites showed no significant difference between the various woody species but did differ significantly between sites. The Proteobacteria phylum was dominant, accounting for over 25 % of the overall relative abundance, followed by Actinobacteria, Bacteroidetes and Gemmatimonadetes. Site was also the main driver of fungal community composition, yet unlike bacteria, tree species identity significantly affected fungal communities. The Betulaceae, Salicaceae and Fagaceae families had a high proportion of Basidiomycota, particularly ectomycorrhizal fungi, and the lowest diversity and richness. The other tree families and the unplanted soil harboured a greater abundance of Ascomycota and Mucoromycota. Consequently, for both bacteria and fungi, the site effect significantly impacted their community richness and composition, while the influence of plants on the richness and composition of rhizospheric microbial communities stayed consistent across sites and was dependent on the microbial kingdom. Finally, we highlighted the importance of considering this contrasting response of plant rhizospheric microbial communities in relation to their host identity, particularly to improve assisted revegetation efforts at contaminated sites.

Vaginal microecology and its role in human papillomavirus infection and human papillomavirus associated cervical lesions.

The vaginal microecology comprises the vaginal microbiome, immune microenvironment, vaginal anatomy, and the cervicovaginal fluid, which is rich in metabolites, enzymes, and cytokines. Investigating its role in the female reproductive system holds paramount significance. The advent of next-generation sequencing enabled a more profound investigation into the structure of the vaginal microbial community in relation to the female reproductive system. Human papillomavirus infection is prevalent among women of reproductive age, and persistent oncogenic HPV infection is widely recognized as a factor associated with cervical cancer. Extensive previous research has demonstrated that dysbiosis of vaginal microbiota characterized by a reduction in Lactobacillus species, heightens susceptivity to HPV infection, consequently contributing to persistent HPV infection and the progression of cervical lesion. Likewise, HPV infection can exacerbate dysbiosis. This review aims to provide a comprehensive summary of current literatures and to elucidate potential mechanisms underlying the interaction between vaginal microecology and HPV infection, with the intention of offering valuable insights for future clinical interventions.

Effect of different types of biochar on soil properties and functional microbial communities in rhizosphere and bulk soils and their relationship with CH4 and N2O emissions.

Biochar as an agricultural soil amendment plays vital roles in mediating methane (CH4) and nitrous oxide (N2O) emissions in soils. The link between different types of biochar, bulk soil, and rhizosphere microbial communities in relation to CH4 and N2O emissions is being investigated in this study. The rice pot experiment was conducted using biochar at two temperatures (300°C and 500°C) in combination with three biochar levels (0, 2, 10% w/w). Soil properties and the abundance of genes associated with CH4 and N2O emissions from both rhizosphere and bulk soils were investigated. The study also aimed to examine the structure of microbial communities (pmoA, nosZ) in rhizosphere and bulk soils whereas CH4 and N2O emissions were monitored while growing rice. Results showed that biochar at 300°C and 10% incorporation significantly increased the CH4 emissions by up to 59% rise compared to the control group. Random Forest analysis revealed that the ratio of mcrA/pmoA along with the abundance of mcrA from both rhizosphere and bulk soils, the abundance of AOA, TN, DOC, and the community composition of pmoA-harboring microorganisms from both bulk and rhizosphere soils were important predictors of CH4 emissions. Therefore, the ratio of mcrA/pmoA in rhizosphere soil and the abundance of AOA in bulk soil were the main factors influencing CH4 emissions. Variation Partitioning Analysis (VPA) results indicated that the effects of these factors on bulk soil were 9% of CH4 emissions variations in different treatments, which contributed more than rhizosphere soils' factors. Moreover, random forest analysis results indicated that the abundance of AOB in bulk soil was the most important predictor influencing N2O emissions. The VPA result revealed that the factors in rhizosphere soil could explain more than 28% of the variations in N2O emissions. Our study highlights that rhizosphere soil has a more significant effect than bulk soil on N2O production. Our findings further the understanding of the link between bulk and rhizosphere attributes, and their impact on CH4 and N2O emissions in paddy soils. In summary, we recommend the application of biochar at 500°C and 2% incorporation rate for agricultural production in the area.

Prokaryotic community dynamics and nitrogen-cycling genes in an oxygen-deficient upwelling system during La Niña and El Niño conditions.

Dissolved oxygen regulates microbial distribution and nitrogen cycling and, therefore, ocean productivity and Earth's climate. To date, the assembly of microbial communities in relation to oceanographic changes due to El Niño Southern Oscillation (ENSO) remains poorly understood in oxygen minimum zones (OMZ). The Mexican Pacific upwelling system supports high productivity and a permanent OMZ. Here, the spatiotemporal distribution of the prokaryotic community and nitrogen-cycling genes was investigated along a repeated transect subjected to varying oceanographic conditions associated with La Niña in 2018 and El Niño in 2019. The community was more diverse during La Niña and in the aphotic OMZ, dominated by the Subtropical Subsurface water mass, where the highest abundances of nitrogen-cycling genes were found. The largest proportion of the Gulf of California water mass during El Niño provided warmer, more oxygenated, and nutrient-poor waters towards the coast, leading to a significant increase of Synechococcus in the euphotic layer compared with the opposite conditions during La Niña. These findings suggest that prokaryotic assemblages and nitrogen genes are linked to local physicochemical conditions (e.g. light, oxygen, nutrients), but also to oceanographic fluctuations associated with ENSO phases, indicating the crucial role of climate variability in microbial community dynamics in this OMZ.

Gut microbiota in relation to frailty and clinical outcomes.

The gut microbiota is involved in several aspects of host health and disease, but its role is far from fully understood. This review aims to unveil the role of our microbial community in relation to frailty and clinical outcomes. Ageing, that is the continuous process of physiological changes that begin in early adulthood, is mainly driven by interactions between biotic and environmental factors, also involving the gut microbiota. Indeed, our gut microbial counterpart undergoes considerable compositional and functional changes across the lifespan, and ageing-related processes may be responsible for - and due to - its alterations during elderhood. In particular, a dysbiotic gut microbiota in the elderly population has been associated with the development and progression of several age-related disorders. Here, we first provide an overview of the lifespan trajectory of the gut microbiota in both health and disease. Then, we specifically focus on the relationship between gut microbiota and frailty syndrome, that is one of the major age-related burdens. Finally, examples of microbiome-based precision interventions, mainly dietary, prebiotic and probiotic ones, are discussed as tools to ameliorate the symptoms of frailty and its overlapping conditions (e.g. sarcopenia), with the ultimate goal of actually contributing to healthy ageing and hopefully promoting longevity.

Metatranscriptomics reveals a shift in microbial community composition and function during summer months in a coastal marine environment

AbstractTemperate coastal marine waters are often thermally stratified from spring through fall but can be dynamic and disrupted by tidal currents and wind‐driven upwelling. These mixing events introduce deeper, cooler water with a higher partial pressure of CO2 (pCO2) and its associated microbial communities to the surface. Anecdotally, these events impact shellfish hatcheries and farms, warranting improved understanding of changes in composition and activity of marine microbial communities in relation to environmental processes. To characterize both compositional and functional changes associated with abiotic factors, here, we generate a reference metatranscriptome from the Strait of Georgia over representative seasons and analyze metatranscriptomic profiles of the microorganisms present within intake water containing different pCO2 levels at a shellfish hatchery in British Columbia from June through October. Abiotic factors studied include pH, temperature, alkalinity, aragonite, calcite, and pCO2. Community composition changes were observed to occur at broad taxonomic levels and most notably to vary with temperature and pCO2. Functional gene expression profiles indicated a strong difference between early (June–July) and late summer (August–October) associated with viral activity. The taxonomic data suggest this could be due to the termination of cyanobacteria and phytoplankton blooms by viral lysis in the late season. Functional analysis indicated fewer differentially expressed transcripts associated with abiotic variables (e.g., pCO2) than with the temporal effect. Microbial composition and activity in these waters vary with both short‐term effects observed alongside abiotic variation and long‐term effects observed across seasons. The analysis of both taxonomy and functional gene expression simultaneously in the same samples by environmental RNA (eRNA metatranscriptomics) provided a more comprehensive view for monitoring water bodies than either would in isolation.

Preliminary data on the bacterial diversity of Dobšinská and Demänovská ice caves (Slovakia)

Our work brings preliminary data on the diversity of microorganisms in Dobšinská and Demänovská ice caves (Slovakia). The caves are located at about 80 km from each other. Demänovská Ice Cave is part of the Demänovské caves system, located in the Demänovská Valley in the Low Tatras National Park. Dobšinská Ice Cave (969m asl), is part of the Stratená Cave System, located on the south-western edge of the Slovak Paradise National Park in the Spiš-Gemer karst. Both caves have been opened for the public during the last decades of the 19th century and are presently intensively visited by tourists [in 2014 alone, Demänovská ice cave was visited by 70,769 tourists (Nudziková 2018)]. There are few reports on the biocenosis of these two caves, the available data referring mainly to the invertebrate fauna (Papáč et al. 2019). In what concerns the microorganisms, up to our investigation, in focus have been only the fungi. Thus, in Dobšinská Ice Cave was reported the presence of species such as Botrytis cinerea and Aspergillus fumigatus isolated from bat guano (Nováková 2006) and the abundance of fungi outside and inside the cave was compared while from Demänovská Ice Cave, based on ITS sequences, Ogórek et al. (2018) reports on the phenotypic and genotypic diversity of airborne fungal spores. Our work complements these two studies adding data on the bacterial diversity from different parts of the two caves and depending on the substrate types (ice blocks and/or sediments). Using Sanger sequencing of the 16S amplicons from DNA isolated from pure bacterial cultures obtained from ice and/or sediments of Demänovská and Dobšinská Ice Caves, we identified 7 and respectively 12 species of bacteria. Surprisingly, only two species where common to both caves. In both Demänovská Ice Cave and Dobšinská Ice Cave the bacterial communities were dominated by Acinetobacter and Bacillus. Beside the identification of the main bacterial groups present in the underground habitats, Illumina sequencing enabled us to build genus heatmaps for the caves, allowing for comparision between various segments of each cave in relation with the specific climate features. When compared, the different types of samples (water, sediment, ice) showed different abundance of bacteria, ice diversity being greater than sediment/water diversity in both Dobšinska and Demänovská ice caves. The chemical composition of the samples (ice and water) is also discussed. This work is the first to bring insights on the bacterial diversity of Demänovská and Dobšinská Ice Caves and we appreciate what it opens new directions of research not only on the evolution of the microbial communities in relation to the climate changes occurred in past times, but also on how intense visiting affects the structures of the microorganisms communities.

Application of 3-nitrooxypropanol and canola oil to mitigate enteric methane emissions of beef cattle results in distinctly different effects on the rumen microbial community

BackgroundThe major greenhouse gas from ruminants is enteric methane (CH4) which in 2010, was estimated at 2.1 Gt of CO2 equivalent, accounting for 4.3% of global anthropogenic greenhouse gas emissions. There are extensive efforts being made around the world to develop CH4 mitigating inhibitors that specifically target rumen methanogens with the ultimate goal of reducing the environmental footprint of ruminant livestock production. This study examined the individual and combined effects of supplementing a high-forage diet (90% barley silage) fed to beef cattle with the investigational CH4 inhibitor 3-nitrooxypropanol (3-NOP) and canola oil (OIL) on the rumen microbial community in relation to enteric CH4 emissions and ruminal fermentation.Results3-NOP and OIL individually reduced enteric CH4 yield (g/kg dry matter intake) by 28.2% and 24.0%, respectively, and the effects were additive when used in combination (51.3% reduction). 3-NOP increased H2 emissions 37-fold, while co-administering 3-NOP and OIL increased H2 in the rumen 20-fold relative to the control diet. The inclusion of 3-NOP or OIL significantly reduced the diversity of the rumen microbiome. 3-NOP resulted in targeted changes in the microbiome decreasing the relative abundance of Methanobrevibacter and increasing the relative abundance of Bacteroidetes. The inclusion of OIL resulted in substantial changes to the microbial community that were associated with changes in ruminal volatile fatty acid concentration and gas production. OIL significantly reduced the abundance of protozoa and fiber-degrading microbes in the rumen but it did not selectively alter the abundance of rumen methanogens.ConclusionsOur data provide a mechanistic understanding of CH4 inhibition by 3-NOP and OIL when offered alone and in combination to cattle fed a high forage diet. 3-NOP specifically targeted rumen methanogens and partly inhibited the hydrogenotrophic methanogenesis pathway, which increased H2 emissions and propionate molar proportion in rumen fluid. In contrast, OIL caused substantial changes in the rumen microbial community by indiscriminately altering the abundance of a range of rumen microbes, reducing the abundance of fibrolytic bacteria and protozoa, resulting in altered rumen fermentation. Importantly, our data suggest that co-administering CH4 inhibitors with distinct mechanisms of action can both enhance CH4 inhibition and provide alternative sinks to prevent excessive accumulation of ruminal H2.

Soil metabolic profile as influenced by seasonal and topographical variations in tropical dry deciduous forest: A biolog based approach

The soil microbial communities and factors therein play important role in maintaining nutrient turnover in forest ecosystem. A biolog ecoplate based approach was applied to a dry deciduous tropical forest to investigate metabolic profile of soil microbial communities in relation to topography and seasonality. Significant (p &lt; 0.05) effect of seasonality on metabolic profile was observed. The average well color development (AWCD), rate of change (r) and metabolic diversity indices (functional diversity indices) were recorded maximum in rainy season followed by winter and summer indicating maximum microbial activity in rainy season. Principal component analysis revealed seasonality to be the major determinant of soil metabolic profile, a key aspect of ecosystem functioning.

Are microbial communities indicators of soil health in a dryland wheat cropping system?

Soil health is an increasingly important concept that provides aspirational targets for agricultural management. Due in part to the incredible diversity of soil microbial communities, however, the biological components of soil health remain poorly understood. In the last decade the refinement of high-throughput DNA sequencing approaches for examining soil microbial communities has led to sequence-variant resolution insights into their diversity. In this work we employ high-throughput sequencing of bacterial (16S rRNA genes) and fungal (internal transcribed spacer [ITS]) regions to evaluate soil microbial communities in relation to other soil chemical parameters, biological soil health tests, and crop yields in fields under long-term reduced tillage (business-as-usual) and no tillage (aspirational) management at two soil depths. We found that tillage systems and soil depth were crucial determinants of microbial community composition and diversity in conjunction with soil chemical measures. Moreover, although some measures of biological soil health (CO2-burst, Haney Soil Health Score) did not differentiate fields under reduced tillage and no-till systems, amplicon sequencing revealed clear differences in microbial communities between management regimes. The relative abundances of many microbial taxa were significantly related to soil chemical variables and crop yields. Fungal communities showed stronger correlations with yield than bacterial communities at both depth increments. Fungi from the families Sordariaceae, Hydnodontaceae, Hypocreaceae, and Clavicipitaceae were positively correlated with yield, especially in the upper soil depth, while Glomeraceae and Phaeosphaeriaceae were negatively correlated. Many of these correlations were also seen in the subsequent winter wheat and chickpea crops, and some correlations could be detected in the 20-year previous yield history of the no-tillage farm. Among the bacteria, only Microbaceriaceae and Xanthomonadaceae were positively correlated, but Caulobacteriaceae, Flavobacteriaceae, Sphingobacteriaceae, Chitinophagaceae were more abundant in lower yielding locations. This may reflect the strong plant selection in the rhizosphere for these bacterial groups in stressed plants. There were no significant differences, however, between microbial diversity and management practices or significant correlations with crop yields. These results suggest that some specific groups of microbial taxa are responsive to tillage systems, exhibit positive relationships with grain yields, and may be useful indicators of soil health.

Change in Abundance and Activity of Microbocenoses in the Area of Influence of a Large Landslide at the Bureya Reservoir

The results of field and experimental microbiological studies of water, soil, and rock samples in the influence zone of large landslide are presented. The landslide occurred in December 2018 and blocked the Bureya Reservoir from coast to coast. An artificial channel was created to restore the hydrological regime with the use of TNT (trinitrotoluene) and RDX (hexogen). A comparative analysis of the abundance of cultivated heterotrophic bacteria around the landslide body and in the artificial channel is carried out. The activity of microbial communities in relation to easily available (peptone, lactate, and starch) and difficult-to-mineralize humic compounds is also determined. With the use of spectrometry and gas chromatography, it is shown that an increase in the diversity of aromatic compounds in water is accompanied by an increase in the abundance of heterotrophic bacteria. A number of toxic substances, including methanol and methylated benzene derivatives, are found among the dominant components in the water. Its concentrations increased after the water drained through the landslide body and after imploding works. Many of the volatile organic compounds may have been products of microbial metabolism when water interacts with rocks. A hypothesis on the role of methanotrophic and methylotrophic bacteria in the genesis of methanol and toluene is discussed.

Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health.

Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.

Identification and Metabolism of Naturally Prevailing Microorganisms in Zinc and Copper Mineral Processing

It has only recently been discovered that naturally prevailing microorganisms have a notable role in flotation in addition to chemical process parameters and overall water quality. This study’s aim was to assess the prevailing microbial communities in relation to process chemistry in a zinc and copper mineral flotation plant. Due to the limitations of cultivation-based microbial methods that detect only a fraction of the total microbial diversity, DNA-based methods were utilised. However, it was discovered that the DNA extraction methods need to be improved for these environments with high mineral particle content. Microbial communities and metabolism were studied with quantitative PCR and amplicon sequencing of bacterial, archaeal and fungal marker genes and shotgun sequencing. Bacteria dominated the microbial communities, but in addition, both archaea and fungi were present. The predominant bacterial metabolism included versatile sulfur compound oxidation. Putative Thiovirga sp. dominated in the zinc plant and the water circuit samples, whereas Thiobacillus spp. dominated the copper plant. Halothiobacillus spp. were also an apparent part of the community in all samples. Nitrogen metabolism was more related to assimilatory than dissimilatory nitrate and nitrite oxidation/reduction reactions. Abundance of heavy metal resistance genes emphasized the adaptation and competitive edge of the core microbiome in these extreme conditions compared to microorganisms freshly entering the process.

Soil organic matter stability and microbial community in relation to different plant cover: A focus on forests characterizing Mediterranean area

In this study, soil organic matter (SOM), as well as the structure and function of soil microbial communities in three forest systems (holm oak, black pine and beech) widely distributed in the Mediterranean area, were analyzed to assess the effects of different canopies on microbial community. Fourier transform infrared (FTIR) spectroscopy, combined with Thermal analyses, was used to characterize SOM, in order to obtain information on its quality and stability. Soil microbial communities were analyzed through the phospholipid fatty acid (PLFA) profile, ergosterol, hydrolase, laccase and peroxidase activities, fungal and bacterial growth. Soil under pine and beech contained more recalcitrant SOM, in respect to the soil under holm oak, characterized by more labile SOM. The PLFA analysis showed a different structure of the edaphic microbial community of the three forests. Soils under pine was characterized by the greatest abundance of fungal biomass and high peroxidase activity likely in relation to the presence in this soil of more recalcitrant compounds, mainly decomposed by fungi. Overall, pine and beech forests represent important carbon sinks with larger amounts of recalcitrant organic matter in their soils.

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog.

The human gut microbiota performs functions that are essential for the maintenance of the host physiology. However, characterizing the functioning of microbial communities in relation to the host remains challenging in reference-based metagenomic analyses. Indeed, as taxonomic and functional analyses are performed independently, the link between genes and species remains unclear. Although a first set of species-level bins was built by clustering co-abundant genes, no reference bin set is established on the most used gut microbiota catalog, the Integrated Gene Catalog (IGC). With the aim to identify the best suitable method to group the IGC genes, we benchmarked nine taxonomy-independent binners implementing abundance-based, hybrid and integrative approaches. To this purpose, we designed a simulated non-redundant gene catalog (SGC) and computed adapted assessment metrics. Overall, the best trade-off between the main metrics is reached by an integrative binner. For each approach, we then compared the results of the best-performing binner with our expected community structures and applied the method to the IGC. The three approaches are distinguished by specific advantages, and by inherent or scalability limitations. Hybrid and integrative binners show promising and potentially complementary results but require improvements to be used on the IGC to recover human gut microbial species.

Microbial Niche Diversification in the Galápagos Archipelago and Its Response to El Niño.

The Galápagos Archipelago is located at the intersection of several major oceanographic features that produce diverse environmental conditions around the islands, and thus has the potential to serve as a natural laboratory for discerning the underlying environmental factors that structure marine microbial communities. Here we used quantitative metagenomics to characterize microbial communities in relation to archipelago marine habitats, and how those populations shift due to substantial environmental changes brought on by El Niño. Environmental conditions such as temperature, salinity, inorganic dissolved nutrients, and dissolved organic carbon (DOC) concentrations varied throughout the archipelago, revealing a diversity of potential microbial niches arising from upwelling, oligotrophic to eutrophic gradients, physical isolation, and potential island mass effects. The volumetric abundances of microbial community members shifted with these environmental changes and revealed several taxonomic indicators of different water masses. This included a transition from a Synechococcus dominated system in the west to an even mix of Synechococcus and Prochlorococcus in the east, mirroring the archipelago’s mesotrophic to oligotrophic and productivity gradients. Several flavobacteria groups displayed characteristic habitat distributions, including enrichment of Polaribacter and Tenacibaculum clades in the relatively nutrient rich western waters, Leeuwenhoekiella spp. that were enriched in the more nutrient-deplete central and eastern sites, and the streamlined MS024-2A group found to be abundant across all sites. During the 2015/16 El Niño event, both environmental conditions and microbial community composition were substantially altered, primarily on the western side of the archipelago due to the reduction of upwelling from the Equatorial Undercurrent. When the upwelling resumed, concentrations of inorganic nutrients and DOC at the western surface sites were more typical of mesopelagic depths. Correspondingly, Synechococcus abundances decreased by an order of magnitude, while groups associated with deeper water masses were enriched, including streamlined roseobacters HTCC2255 and HIMB11, Thioglobacaceae, methylotrophs (Methylophilaceae), archaea (Nitrosopumilaceae), and distinct subpopulations of Pelagibaceriales (SAR11 clade). These results provide a quantitative framework to connect community-wide microbial volumetric abundances to their environmental drivers, and thus incorporation into biogeochemical and ecological models.

Metagenomic data of soil microbial community in relation to basal stem rot disease.

The oil palm industry, especially in Indonesia and Malaysia is being threatened by Basal Stem Rot (BSR) disease caused by Ganoderma boninense. There is no conclusive remedy in handling this disease effectively. In this study, metagenomics analysis of soil were analyzed for a better understanding of the microbial diversity in relation to BSR disease. Study was conducted in three plantation sites of Sabah, Malaysia which incorporated different disease management and agronomic practices. The estates are located at Sandakan (Kam Cheong Plantation), Lahad Datu (FGV Ladang Sahabat) and Tawau (Warisan Gagah). Soil samples were collected from disease free, high and low BSR incidence plots. Illumina MiSeq metagenomic analysis using V3–V4 region of 16S rRNA gene was employed to study the microbial diversity. Bacteria (97.4%) and Archaea (0.2%) were found majority in kingdom taxonomy level. The most abundant phyla were Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia. Higher alpha diversity of all species was observed among all tested soil from each estates. Beta analysis was analyzed using non phylogenetic UnifRac matrix and visualized using Principal Coordinates Analysis (PCoA). The tested soil samples in Kam Cheong Plantation were found to have similar bacterial communities. The data provided is useful as an indicator in developing biology controls against Ganoderma boninense.