Phylotype Richness Research Articles

Functional Guilds, Community Assembly, and Co-occurrence Patterns of Fungi in Metalliferous Mine Tailings Ponds in Mainland China.

Metalliferous mine tailings ponds are generally characterized by low levels of nutrient elements, sustained acidic conditions, and high contents of toxic metals. They represent one kind of extreme environments that are believed to resemble the Earth's early environmental conditions. There is increasing evidence that the diversity of fungi inhabiting mine tailings ponds is much higher than previously thought. However, little is known about functional guilds, community assembly, and co-occurrence patterns of fungi in such habitats. As a first attempt to address this critical knowledge gap, we employed high-throughput sequencing to characterize fungal communities in 33 mine tailings ponds distributed across 18 provinces of mainland China. A total of 5842 fungal phylotypes were identified, with saprotrophic fungi being the major functional guild. The predictors of fungal diversity in whole community and sub-communities differed considerably. Community assembly of the whole fungal community and individual functional guilds were primarily governed by stochastic processes. Total soil nitrogen and total phosphorus mediated the balance between stochastic and deterministic processes of the fungal community assembly. Co-occurrence network analysis uncovered a high modularity of the whole fungal community. The observed main modules largely consisted of saprotrophic fungi as well as various phylotypes that could not be assigned to known functional guilds. The richness of core fungal phylotypes, occupying vital positions in co-occurrence network, was positively correlated with edaphic properties such as soil enzyme activity. This indicates the important roles of core fungal phylotypes in soil organic matter decomposition and nutrient cycling. These findings improve our understanding of fungal ecology of extreme environments.

Vegetation restoration increases the diversity of bacterial communities in deep soils

Soil microbial communities are engineers of key biogeochemical processes and mediate the functioning of vegetation restoration ecosystems following cropland abandonment. However, how microbial communities in the deep soil profile, especially the complexity and stability of their interactions, respond to vegetation restoration remains unclear. Here, we explored the soil properties and bacterial community diversity, structure, and network interactions and attempted to identify the keystone taxa along the 0–500 cm soil profile under different land use types (cropland, restored woodland, restored grassland). The results showed soil bacterial alpha diversity, indicated by phylotype richness and Shannon diversity index, was higher in deeper soil layers under restored lands (woodland and grassland) compared to long-term cultivated cropland. The dominant phyla of bacterial communities included Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and GAL15. Using the molecular ecological network approach, we confirmed bacterial ecological networks were more complex in restored woodland and grassland, compared to cropland, indicating the bacterial species have greater niche-sharing and more interactions over the whole 0–500 cm profile under restored ecosystems. Moreover, relatively large and intricate bacterial interactions persisted in the soil deep layer (380–400 cm). Soil available phosphorus (P), organic carbon, and total P contents, fine root length density, and soil moisture conditions strongly affected microbial communities after vegetation restoration. In general, our findings have implications for understanding the potential of restored ecosystems to withstand disturbances under global climate change scenarios.

Natural Environmental Variation Determines Microbial Diversity Patterns in Serofluid Dish, a Traditional Chinese Fermented Vegetable Food.

Serofluid dish is a traditional fermented food that contains rich microbial populations. To gain insight into the environmental variables shaping the microbial diversity patterns, serofluid dish samples were collected from different areas, and 16S rRNA sequencing was performed. Analyses revealed both species and community diversity, including phylotype richness, Shannon index and phylogenetic diversity, were mostly influenced by pH. Additionally, such effects were corroborated by the Mantel test of pairwise UniFrac distances and variable selection of multiple linear regression models. Eventually, correlations between dominant lineages and the pH of serofluid dish other than geographical distance explained a large portion of the changes in microbial composition and diversity. Lactobacillus and related genera, Pediococcus and Acetobacter were largely driven by the variability of pH, and higher richness was observed under moderate pH ranges. Collectively, the results demonstrated that a microbial diversity pattern in serofluid dish is predictable by natural environmental variation and can be better understood through pH conditions.

Niche Partitioning of Labyrinthulomycete Protists Across Sharp Coastal Gradients and Their Putative Relationships With Bacteria and Fungi.

While planktonic microbes play key roles in the coastal oceans, our understanding of heterotrophic microeukaryotes’ ecology, particularly their spatiotemporal patterns, drivers, and functions, remains incomplete. In this study, we focus on a ubiquitous marine fungus-like protistan group, the Labyrinthulomycetes, whose biomass can exceed that of bacterioplankton in coastal oceans but whose ecology is largely unknown. Using quantitative PCR and amplicon sequencing of their 18S rRNA genes, we examine their community variation in repeated five-station transects across the nearshore-to-offshore surface waters of North Carolina, United States. Their total 18S rRNA gene abundance and phylotype richness decrease significantly from the resource-rich nearshore to the oligotrophic offshore waters, but their Pielou’s community evenness appears to increase offshore. Similar to the bacteria and fungi, the Labyrinthulomycete communities are significantly structured by distance from shore, water temperature, and other environmental factors, suggesting potential niche partitioning. Nevertheless, only several Labyrinthulomycete phylotypes, which belong to aplanochytrids, thraustochytrids, or unclassified Labyrinthulomycetes, are prevalent and correlated with cohesive bacterial communities, while more phylotypes are patchy and often co-occur with fungi. Overall, these results complement previous time-series observations that resolve the Labyrinthulomycetes as persistent and short-blooming ecotypes with distinct seasonal preferences, further revealing their partitioning spatial patterns and multifaceted roles in coastal marine microbial food webs.

Phylotype diversity within soil fungal functional groups drives ecosystem stability.

Soil fungi are fundamental to plant productivity, yet their influence on the temporal stability of global terrestrial ecosystems, and their capacity to buffer plant productivity against extreme drought events, remain uncertain. Here we combined three independent global field surveys of soil fungi with a satellite-derived temporal assessment of plant productivity, and report that phylotype richness within particular fungal functional groups drives the stability of terrestrial ecosystems. The richness of fungal decomposers was consistently and positively associated with ecosystem stability worldwide, while the opposite pattern was found for the richness of fungal plant pathogens, particularly in grasslands. We further demonstrated that the richness of soil decomposers was consistently positively linked with higher resistance of plant productivity in response to extreme drought events, while that of fungal plant pathogens showed a general negative relationship with plant productivity resilience/resistance patterns. Together, our work provides evidence supporting the critical role of soil fungal diversity to secure stable plant production over time in global ecosystems, and to buffer against extreme climate events.

Characterization of persistent organic pollutants and culturable and non-culturable bacterial communities in pulp and paper sludge after secondary treatment

Due to the presence of various organic contaminants, improper disposal of pulp-paper wastewater poses harm to the environment and human health. In this work, pulp-paper sludge (PPS) after secondary treatment were collected from M/s Century Pulp-paper Mills in India, the chemical nature of the organic pollutants was determined after solvent extraction. All the isolates were able to produce lipase (6.34–3.93 U ml−1) which could account for the different fatty acids detected in the PPS. The dominant strains were in the classes of α and γ Proteobacteria followed by Firmicutes. The Shannon-Weiner diversity indexes for phylotype richness for the culturable and non-culturable bacterial community were 2.01 and 3.01, respectively, indicating the non-culturable bacterial strains has higher species richness and diversity compared to the culturable bacterial strains. However, the culturable strains had higher species evenness (0.94 vs 0.90). Results suggested only a few isolated strains were resistant to the POPs in the PPS, where as non-cultural bacteria survived by entering viable but non-cultural state. The isolated strains (Brevundimonas diminuta, Aeromonas punctata, Enterobacter hormaechei, Citrobacter braakii, Bacillus pumilus and Brevundimonas terrae) are known for their multidrug resistance but their tolerance to POPs have not previously been reported and deserved further investigation. The findings of this research established the presence of POPs which influence the microbial population. Tertiary treatment is recommended prior to the safe disposal of pulp paper mill waste into the environment.

Comparative lactic acid bacteria (LAB) profiles during dadih fermentation with spontaneous and back-slopping methods, as identified by terminal-restriction fragment length polymorphism (T-RFLP)

The diversity of lactic acid bacteria (LAB) present during the manufacture of traditional fermented buffalo milk from West Sumatra, known as dadih, was studied via a culture-independent approach using terminal-restriction fragment length polymorphism (T-RFLP) to compare the dynamic diversity in back-slopping and spontaneous fermentation methods. Total LAB and pH were measured in freshly prepared buffalo milk and in \textit{dadih} fermented for 24 and 48 hours. The results indicated significant differences between the fermentation methods, with higher total LAB, and greater phylotype richness and relative abundance being identified in the back-slopping method. Terminal fragment lengths (TRFs) of 68 and 310 bp were common to both techniques, similar to those of Lactobacillus fermentum, Fructobacillus pseudoficulneus, Leuconostoc citreum, Leuconostoc kimchii, and Leuconostoc sp. The changes in phylotype number (species number) and relative abundances of LAB communities identified are expected to produce data needed to formulate the best fermentation process for dadih manufacturing. A 24-hour back-slopping fermentation method is recommended, as fermentation time of longer than 24 hours reduced viable LAB significantly. Our results also indicated that the T-RFLP technique is not only clearly sensitive enough and adequate for segregating LAB diversity in both fermentation methods, but that it also provides good information regarding the structure of microbial communities and their composition change during the fermentation process.

Soil type and pH mediated arable soil bacterial compositional variation across geographic distance in North China Plain

A challenge in biogeography is to understand what are the factors and how they regulate soil microbial communities. To explore the coexistence pattern of bacterial community and the factors shaping agricultural soil bacterial community at spatial scale, 135 soil samples were collected from a typically agricultural province in the North China Plain and analyzed with high-throughput 16S rRNA gene sequencing. As expected, bacterial community dissimilarity showed significant distance-decay relationships with 42.2% variation explained by geographic distance and physicochemical factors. Bacterial phyla abundance showed different responses to environmental factors among which soil pH was the primary factor shaping soil bacterial community structure. Bacterial communities in acidic soils suggest lower phylotype richness and phylogenetic diversity and its associated network structure showed greater connectivity and stability compared to those in neutral and alkaline soils. Soil bacterial community diversity was also varied with soil type. Unlike the simplest topological features of co-occurrence network in Cinnamon soil, bacterial community structure was more connected and stable in Lime concretion black soil and Kallotenuales but not the predominant taxa were identified as kinless hub. However, Neisseriales, Anaerolineaceae and Nannocystaceae from Proteobacteria and Chloroflexi with higher relative abundance might support higher levels of ecosystem functions in Fluvo-aquic soil. Taken together, our results suggest that geographic distance and pH variation strongly shaped bacterial community structure with correspondingly diverse co-occurrence patterns observed in different soil pH ranges and types.

Associations Between Gut Microbiota and Asthma Endotypes: A Cross-Sectional Study in South China Based on Patients with Newly Diagnosed Asthma.

ObjectiveThis study aimed to investigate the gut microbiome profile in different inflammatory phenotypes of treatment-naive newly diagnosed asthmatic adults, to gain insight on the associations between intestinal microbiota and phenotypic features that characterize asthma heterogeneity to develop new treatments for asthma.MethodsFresh stool samples were obtained from 20 healthy subjects and 47 newly diagnosed asthmatic patients prior to any interventions. The asthmatics were divided into allergic and non-allergic cohorts. Intestinal microbiota was analyzed by 16S rRNA next-generation sequencing. Demographic and clinical parameters were collected. Alpha and beta diversity analysis were calculated to detect differences within sample phylotype richness and evenness between controls and asthmatic patients. Statistically significant differences between samples were analyzed for all used metrics, and features of gut bacterial community structure were evaluated in relation to extensive clinical characteristics of asthmatic patients.ResultsGut microbial compositions were significantly different between asthmatic and healthy groups. Alpha-diversity of the gut microbiome was significantly lower in asthmatics than in controls. The microbiome between allergic and non-allergic asthmatic patients were also different, and 28 differential species were identified. PPAR signaling pathway, carotenoid biosynthesis, and flavonoid biosynthesis were significantly positively correlated with allergy-associated clinical index, including FENO value, blood eosinophil counts, and serum IgE and IL-4 levels. A combination of Ruminococcus bromii, Brevundimonas vesicularis, and Clostridium disporicum showed an AUC of 0.743 in the specific allergic/non-allergic cohort. When integrating C. disporicum, flavone, flavonol biosynthesis, and serum IL-4 values, the AUC achieved 0.929 to classify asthmatics. At the same time, C. colinum and its associated functional pathway exhibited an AUC of 0.78 to distinguish allergic asthmatics from those without allergies.ConclusionWe demonstrated a distinct taxonomic composition of gut microbiota in different asthmatic phenotypes, highlighting their significant relationships. Our study may support considerations of intestinal microbial signatures in delineating asthma phenotypes.

Environment-host-microbial interactions shape the Sarracenia purpurea microbiome at the continental scale.

The importance of climate, habitat structure, and higher trophic levels on microbial diversity is only beginning to be understood. Here, we examined the influence of climate variables, plant morphology, and the abundance of aquatic invertebrates on the microbial biodiversity of the northern pitcher plant Sarracenia purpurea. The plant's cup-shaped leaves fill with rainwater and support a miniature, yet full-fledged, ecosystem with a diverse microbiome that decomposes captured prey and a small network of shredding and filter-feeding aquatic invertebrates that feed on microbes. We characterized pitcher microbiomes of 108 plants sampled at 36 sites from Florida to Quebec. Structural equation models revealed that annual precipitation and temperature, plant size, and midge abundance had direct effects on microbiome taxonomic and phylogenetic diversity. Climate variables also exerted indirect effects through plant size and midge abundance. Further, spatial structure and climate influenced taxonomic composition, but not phylogenetic composition. Our results suggest that direct effects of midge abundance and climate and indirect effects of climate through its effect on plant-associated factors lead to greater richness of microbial phylotypes in warmer, wetter sites.

Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand.

The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).

Effect of land use changes on soil microbial enzymatic activity and soil microbial community composition on Maryland's Eastern Shore

We compared microbial enzymatic activity and community composition in small, undisturbed, family cemetery soils and surrounding agricultural fields or suburban lawns to determine the effect of land use changes on soil biology. We collected soil from seven sites in Wicomico County, Maryland monthly for one year. Fluorescein diacetate (FDA) hydrolysis and dehydrogenase activity were significantly greater in the cemetery soils compared to field soils (agricultural and lawn) 63% and 30% of the time, respectively. Much less frequently the field soils had significantly higher microbial activity compared to the cemetery soils (10% of sample pairs for both FDA and dehydrogenase). FDA activity measurements were highest in the spring and lowest in late summer at all seven sites, while no seasonal variation was evident for dehydrogenase activity. Dominant bacterial phyla in the soils were similar between field and cemetery sites with the exception of Gemmatimonadetes having higher relative abundance in fields. Fourteen genera differed in relative abundance between cemeteries and fields, and the relative abundance of these genera correlated with soil pH, organic matter, and phosphorus levels. There was no difference in phylotype richness or diversity between fields and cemetery soils. Based on FDA hydrolysis, microbial activity is greater in cemetery soils, providing evidence to suggest land use changes have altered the biological properties of these soils.

Three-dimensional carbon-based anodes promoted the accumulation of exoelectrogens in bioelectrochemical systems.

To achieve deep understandings on the effects of structure and surface properties of anode material on the performance of bioelectrochemical systems, the present research investigated the bacterial community structures of biofilms attached to different three-dimensional anodes including carbon felt and materials derived from pomelo peel, kenaf stem, and cardboard with 454 pyrosequencing analysis based on the bacterial 16S rRNA gene. The results showed that bacterial community structures, especially the relative abundance of exoelectrogens, were significantly related to the types of adopted three-dimensional anode materials. Proteobacteria was the shared predominant phylum, accounting for 55.4%, 52.1%, 66.7%, and 56.1% for carbon felt, cardboard, pomelo peel, and kenaf stem carbon, respectively. The most abundant OTU was phylogenetically related to the well-known exoelectrogen of Geobacter, with a relative abundance of 16.3%, 19.0%, 36.3%, and 28.6% in carbon felt, cardboard, pomelo peel, and kenaf stem, respectively. Moreover, another exoelectrogen of Pseudomonas sp. accounted for 4.9% in kenaf stem and 3.9% in carbonboard, respectively. The results implied the macrostructure and properties of different anode materials might result in different niches such as hydrodynamics and substrate transport dynamics, leading to different bacterial structure, especially different relative abundance of exoelectrogens, which consequently affected the performance of bioelectrochemical systems. PRACTITIONER POINTS: Bioelectrochemical systems (BESs) represent a novel biotechnology platform to simultaneously treat wastewaters and produce electrical power. Three-dimensional materials derived from nature plant as anode to promote electricity output from BESs and reduce the construct cost of BESs. Macrostructure of the three-dimensional anode material affected phylotype richness and phylogenetic diversity of microorganisms in anodic biofilm of BESs. Geobacter as well-known exoelectrogen was the most abundant in biofilm attached to three-dimensional anode.

Pyrosequencing investigation into the bacterial communities in the Qinghai-Tibet Plateau soils associated with soil characteristic factors

The Qinghai Tibet Plateau (QTP) is one of the most important regions of the earth’s ecosystem that is vulnerable to climate and human activities due to its complex climate and terrain. However, knowledge about soil bacterial communities and their effect on the ecosystem within the QTP environments is still scarce. Metagenomic approaches on the structure and diversity of bacterial communities and their relationship with the environment from eighteen selected sites of the five major QTP ecosystems (gray-cinnamon soils, chernozems, castanozems, mountain meadow soils, gray desert soils) are presented in this paper. The dominant bacterial phyla in five type soils were Proteobacteria and Actinobacteria, whereas Actinobacteria and Chloroflexi predominated in gray desert soils. The bacteria diversity in castanozeras and mountain meadow soils was significantly higher than that of the other three soil types (P < 0.05). Phylogenetic diversity in gray desert soil was significantly lower than that of other four soil types (P < 0.05). Phylotype richness was the lowest in gray-cinnamon soils. There were significant correlations between the phylotype richness and soil moisture (r = -0.578) and potassium (r = -0.529). Phylogenetic diversity (PD) was significantly correlated with total organic carbon (r = -0.548). The redundancy analysis (RDA) showed that the diversity and composition in the bacterial communities differed greatly among the five soil types and that they were closely correlated with the soil moisture, soil organic carbon and potassium. These results indicated that the bacterial community structures of QTP soils were obviously influenced by soil characteristics and soil environmental characteristics and provided a theoretical basis for the optimal management and sustainable utilization of the QTP soil ecosystem, which is of great significance.

Response of stream fungi on decomposing leaves to experimental drying

AbstractClimate change may lead to increased droughts in the future, which in turn may lead to increased periods of stream drying. We conducted an experiment to test the effects of drying on fungal communities and microbial activity on decaying leaves from a stream. Our experimental setup included immersion of maple leaf cores for 2 weeks in a small stream to allow for the colonization of microbes. Leaves were then subjected for 2 weeks to four treatments: one control, where leaves stayed immersed in the stream, and three drying treatments in different settings (field, lab, and oven). Leaves were then returned to sterile water for 2 weeks of recovery. Microbial respiration declined after all drying treatments compared to the control, with the oven‐dried leaves taking the longest time to recover. All drying treatments had similar respiration to each other and the control after 2 weeks of immersion recovery. Fungal communities on the leaves were assessed by polymerase chain reaction amplification of fungal DNA from leaves followed by denaturing gradient gel electrophoresis (DGGE). Most treatments had very similar communities based on phylotypes from DGGE, with little change during drying and recovery compared to immersion controls. However, the oven‐dried leaves had a very different community developing during recovery. There were no differences in diversity or richness of DGGE phylotypes among treatments after recovery. Overall, the fungal communities, in our experiment, appeared resilient to the effects of short‐term drying, with little change to community structure and relatively fast recovery in activity after rewetting.

Differences in the intestinal microbiome of healthy children and patients with newly diagnosed Crohn\u2019s disease

The aetiology of inflammatory bowel diseases (IBD) seems to be strongly connected to changes in the enteral microbiome. The dysbiosis pattern seen in Crohn’s disease (CD) differs among published studies depending on patients’ age, disease phenotype and microbiome research methods. The aims was to investigate microbiome in treatment-naive paediatric patients to get an insight into its structure at the early stage of the disease in comparison to healthy. Stool samples were obtained from controls and newly diagnosed patients prior to any intervention. Microbiota was analysed by 16SrRNAnext-generation-sequencing (NGS). Differences in the within-sample phylotype richness and evenness (alpha diversity) were detected between controls and patients. Statistically significant dissimilarities between samples were present for all used metrics. We also found a significant increase in the abundance of OTUs of the Enterococcus genus and reduction in, among others, Bifidobacterium (B. adolescentis), Roseburia (R.faecis), Faecalibacterium (F. prausnitzii), Gemmiger (G. formicilis), Ruminococcus (R. bromii) and Veillonellaceae (Dialister). Moreover, differences in alpha and beta diversities in respect to calprotectin and PCDAI were observed: patients with calprotectin <100 µg/g and with PCDAI below 10 points vs those with calprotectin >100 µg/g and mild (10–27.7 points), moderate (27.5–40 points) or severe (>40 points) CD disease activity had higher richness and diversity of gut microbiota. The results of our study highlight reduced diversity and dysbiosis at the earliest stage of the disease. Microbial imbalance and low abundance of butyrate-producing bacteria, including Bifidobacterium adolescentis, may suggest benefits of microbial modification therapy.

Towards a simple global-standard bioassay for a key ecosystem process: organic-matter decomposition using cotton strips

Abstract Cotton-strip bioassays are increasingly used to assess ecosystem integrity because they provide a standardized measure of organic-matter decomposition – a fundamental ecosystem process. However, several different cotton-strip assays are routinely used, complicating the interpretation of results across studies, and hindering broader synthesis. Here, we compare the decay rates and assemblages of bacteria and fungi colonizing the three most commonly used cotton materials: Artist’s canvas, Calico cloth, and Empa fabric. Cotton strips from each material type were incubated in 10 streams that span a wide range of physicochemical properties across five ecoregions. Additionally, to evaluate responses to environmental stress without potentially confounding biogeographical effects, we deployed identical bioassays in five streams across an acidification gradient within a single ecoregion. Across all streams decomposition rates (as tensile strength loss [TSL]) differed among the three cotton materials; Calico cloth decomposed fastest (time to 50% TSL [T50] = 16.7 d), followed by the Empa fabric (T50 = 18.3 d) and then Artist’s canvas (T50 = 21.4 d). Despite these differences, rates of TSL of the three cotton materials responded consistently to variation in environmental conditions; TSL of each fabric increased with stream temperature, dissolved-nutrient concentrations and acid-neutralizing capacity, although Artist’s canvas and Calico cloth were more sensitive than Empa fabric. Microbial communities were similar among the materials, and values of community structure (e.g., phylotype richness and diversity) were comparable to those reported for decaying leaves in streams from the same region, the major natural basal carbon resource in forested-stream ecosystems. We present linear calibrations among pairs of assays so that past and future studies can be expressed in a “common currency” (e.g., Artist’s-fabric equivalents) ‘past and future studies’ repeated two times in the sentence. Lastly, given its relatively low within-site variability, and the large number of streams where it has been used (>700 across the globe), we recommend Artist’s fabric for future work. These results show that cotton provides an effective and realistic standardized substrate for studying heterotrophic microbial assemblages, and acts as a reasonable proxy for more chemically complex forms of detritus. These findings add to growing evidence that cotton-strip bioassays are simple, effective and easily standardized indicators of heterotrophic microbial activity and the ecosystem processes that result.

Contrasted Micro-Eukaryotic Diversity Associated with Sphagnum Mosses in Tropical, Subtropical and Temperate Climatic Zones.

Sphagnum-dominated ecosystem plays major roles as carbon sinks at the global level. Associated microbial communities, in particular, eukaryotes, play significant roles in nutrient fixation and turnover. In order to understand better the ecological processes driven by these organisms, the first step is to characterise these associated organisms. We characterised the taxonomic diversity, and from this, inferred the functional diversity of microeukaryotes in Sphagnum mosses in tropical, subtropical and temperate climatic zones through an environmental DNA diversity metabarcoding survey of the V9 region of the gene coding for the RNA of the small subunit of the ribosomes (SSU rRNA). As microbial processes are strongly driven by temperatures, we hypothesised that saprotrophy would be highest in warm regions, whereas mixotrophy, an optimal strategy in oligotrophic environments, would peak under colder climates. Phylotype richness was higher in tropical and subtropical climatic zones than in the temperate region, mostly due to a higher diversity of animal parasites (i.e. Apicomplexa). Decomposers, and especially opportunistic yeasts and moulds, were more abundant under warmer climates, while mixotrophic organisms were more abundant under temperate climates. The dominance of decomposers, suggesting a higher heterotrophic activity under warmer climates, is coherent with thegenerally observed faster nutrient cycling at lower latitudes; this phenomenon is likely enhanced by higher inputs of nutrients most probably brought in the system by Metazoa, such as arthropods.

Difference in soil bacterial community composition depends on forest type rather than nitrogen and phosphorus additions in tropical montane rainforests

Rapid increase of nitrogen (N) deposition could alter nutrient availability, leading to changes in soil microbial processes and ecosystem carbon and nutrient cycling. However, the effects of N deposition on soil microbes remain elusive in the tropical rainforests in Asia. Here, we conducted a 3-year N addition experiment with four treatments (0, 20, 50, and 100 kg N ha−1 year−1) in a primary and secondary tropical montane forest in Hainan Island, China, to explore the effects of elevated N availability on soil microbial community composition. We also conducted a phosphorus (P) treatment (50 kg P ha−1 year−1) and a N + P treatment (50 kg N ha−1 year−1 + 50 kg P ha−1 year−1) to examine potential P limitation driven by N deposition in highly weathered tropical soils, using a bar-coded pyrosequencing technique. The composition of soil bacterial communities differed dramatically between the primary and secondary forests, but not significant dissimilarity among the fertilization treatments. The community composition, phylogenetic diversity and phylotype richness were significantly correlated with soil pH, total organic C (TOC), and total N (TN), respectively. There were significant differences between the primary and secondary forest in pH, TOC, and TN, but not among the fertilization treatments. These results suggest that differences in soil nutrient status between the primary and secondary forests due to different successional stages rather than chronic N fertilization may be the major factor affecting soil bacterial composition in the tropical montane rainforests.

Soil available phosphorus content drives the spatial distribution of archaeal communities along elevation in acidic terrace paddy soils

Archaea play crucial roles in geochemical cycles and influence the emission of greenhouse gases in acidic soils. However, little is known about the distribution pattern of total archaeal diversity and community composition with increasing elevation, especially in acidic agricultural ecosystems. Terraces, characterized by vertical climate changes and unique hydrological properties, are “natural experiments” to explore the spatial distribution of microorganisms along elevation in paddy soils. Here we investigated the diversity and structure of soil archaeal communities in nine increasingly elevated acidic paddy soils of the Yunhe terrace, China. Archaeal communities were dominated by Methanomicrobia of Euryarchaeota (38.5%), Group 1.1a-associated cluster (SAGSCG-1) of Thaumarchaeota (22.0%) and Subgroup-6 (previously described as crenarchaeotal group 1.3b) of Bathyarchaeota (17.8%). The archaeal phylotype richness decreased with increasing elevation. Both the species richness and phylogenetic diversity of the archaeal communities were significantly negatively correlated with soil available phosphorus (AP) content according to linear regression analyses. The archaeal communities differed greatly between soils of increasing elevation, and were roughly clustered into three groups, mostly in relation to AP contents. A variation partitioning analysis further confirmed that edaphic factors including the content of AP (17.1%), nitrate (7.83%), soil organic carbon (4.69%), dissolved organic carbon (4.22%) and soil pH (4.07%) shaped the archaeal community. The variation of soil properties were probably induced by elevation. The co-occurrence network indicated a modular structure of the archaeal community. Overall, our results emphasized that soil AP content was the best predictor of archaeal diversity and community structure, and the impacts of elevation on soil archaeal communities were not diminished by long-term rice cultivation, although minor compared with the effects of soil properties.