Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits.

Revealing the mechanisms underlying soil microbial community assembly is a fundamental objective in molecular ecology. However, despite increasing body of research on overall microbial community assembly mechanisms, our understanding of subcommunity assembly mechanisms for different prokaryotic and fungal taxa remains limited. Here, soils were collected from more than 100 sites across southwestern China. Based on amplicon high-throughput sequencing and iCAMP analysis, we determined the subcommunity assembly mechanisms for various microbial taxa. The results showed that dispersal limitation and homogenous selection were the primary drivers of soil microbial community assembly in this region. However, the subcommunity assembly mechanisms of different soil microbial taxa were highly variable. For instance, the contribution of homogenous selection to Crenarchaeota subcommunity assembly was 70%, but it was only around 10% for the subcommunity assembly of Actinomycetes, Gemmatimonadetes and Planctomycetes. The assembly of subcommunities including microbial taxa with higher occurrence frequencies, average relative abundance and network degrees, as well as wider niches tended to be more influenced by homogenizing dispersal and drift, but less affected by heterogeneous selection and dispersal limitation. The subcommunity assembly mechanisms also varied substantially among different functional guilds. Notably, the subcommunity assembly of diazotrophs, nitrifiers, saprotrophs and some pathogens were predominantly controlled by homogenous selection, while that of denitrifiers and fungal pathogens were mainly affected by stochastic processes such as drift. These findings provide novel insights into understanding soil microbial diversity maintenance mechanisms, and the analysis pipeline holds significant value for future research.

A critical review of soil algae as a crucial soil biological component of high ecological and economic significance.

Aero-terrestrial algae are ecologically and economically valuable bioresources contributing to carbon sequestration, sustenance of soil health, and fertility. Compared to aquatic algae, the literature on subaerial algae is minimal, including studies of distinctive habitats such as forest soils, agricultural fields, deserts, polar regions, specific subaerial zones, artificial structures, and tropical soils. The primary goal here was to identify the gaps and scope of research on such algae. Accordingly, the literature was analyzed per sub-themes, such as the "nature of current research data on terrestrial algae," "methodological approaches," "diversity," "environmental relationships," "ecological roles," and "economic significance." The review showed there is a high diversity of algae in soils, especially members belonging to the Cyanophyta (Cyanobacteria) and Chlorophyta. Algal distributions in terrestrial environments depend on the microhabitat conditions, and many species of soil algae are sensitive to specific soil conditions. The ecological significance of soil algae includes primary production, the release of biochemical stimulants and plant growth promoters into soils, nitrogen fixation, solubilization of minerals, and the enhancement and maintenance of soil fertility. Since aero-terrestrial habitats are generally stressed environments, algae of such environments can be rich in rare metabolites and natural products. For example, epilithic soil algae use wet adhesive molecules to fix them firmly on the substratum. Exploring the ecological roles and economic utility of soil and other subaerial algae could be helpful for the development of algae-based industries and for achieving sustainable soil management.

Soils in warmer and less developed countries have less micronutrients globally.

Soil micronutrients are capital for the delivery of ecosystem functioning and food provision worldwide. Yet, despite their importance, the global biogeography and ecological drivers of soil micronutrients remain virtually unknown, limiting our capacity to anticipate abrupt unexpected changes in soil micronutrients in the face of climate change. Here, we analyzed >1300 topsoil samples to examine the global distribution of six metallic micronutrients (Cu, Fe, Mn, Zn, Co and Ni) across all continents, climates and vegetation types. We found that warmer arid and tropical ecosystems, present in the least developed countries, sustain the lowest contents of multiple soil micronutrients. We further provide evidence that temperature increases may potentially result in abrupt and simultaneous reductions in the content of multiple soil micronutrients when a temperature threshold of 12-14°C is crossed, which may be occurring on 3% of the planet over the next century. Altogether, our findings provide fundamental understanding of the global distribution of soil micronutrients, with direct implications for the maintenance of ecosystem functioning, rangeland management and food production in the warmest and poorest regions of the planet.

Subinhibitory effects of 2,4-diacetylphloroglucinol on filamentous fungus Aspergillus fumigatus.

AIMS: Aspergillus fungi are common members of the soil microbiota. Some physiological and structural characteristics of Aspergillus species make them important participants in soil ecological processes. In this study, we aimed to evaluate the impact of 2,4-diacetylphloroglucinol (2,4-DAPG), a common metabolite of soil and rhizosphere bacteria, on the physiology of Aspergillus fumigatus. METHODS AND RESULTS: Integrated analysis using microscopy, spectrophotometry, and liquid chromatography showed the following effects of 2,4-DAPG on Aspergillus physiology. It was found that A. fumigatus in the biofilm state is resistant to high concentrations of 2,4-DAPG. However, experimental exposure led to a depletion of the extracellular polymeric substance, changes in the structure of the cell wall of the mycelium (increase in the content of α- and ß-glucans, chitin, and ergosterol), and conidia (decrease in the content of DHN-melanin). 2,4-DAPG significantly reduced the production of mycotoxins (gliotoxin and fumagillin) but increased the secretion of proteases and galactosaminogalactan. CONCLUSIONS: Overall, the data obtained suggest that 2,4-DAPG-producing Pseudomonas bacteria are unlikely to directly eliminate A. fumigatus fungi, as they exhibit a high level of resistance when in the biofilm state. However, at low concentrations, 2,4-DAPG significantly alters the physiology of aspergilli, potentially reducing the adaptive and competitive capabilities of these fungi.

The impact of novel azotobacter Bacillus sp. T28 combined sea buckthorn pomace on microbial community structure in paddy soil.

Nitrogen (N) fertilizer application is an essential part of agricultural production in order to improve rice yields. However, long-term irrational application and low utilization of N fertilizer have caused a series of environmental problems. Biofertilizer is considered an effective alternative to N fertilizer. In this study, the effect of biofertilizer made of diazotrophic bacteria Bacillus sp. T28 combined with sea buckthorn pomace on the soil N changes and microbial community structure was conducted. Compared to CK, NO3--N content decreased 33.1%-43.8% and the rate of N2O release decreased 8-26 times under different fertilizer treatments during incubation of 0-7 days. On the contrary, NH4+-N in T28 with or without sea buckthorn pomace treatments increased by 56.5-118.8% during incubation of 7-14 days. The results indicated that this biofertilizer reduced the environmental risk associated with the accumulation of NO3--N in paddy soil and the release of N2O to the atmosphere and maintained the soil available N supply capacity. Besides, applying Bacillus T28 with sea buckthorn pomace increased the abundance of soil N functional genes such as nifH, narG, nirS, nirK, and nosZ. The 13C-PLFAs results demonstrated that this biofertilizer improves soil microbial community diversity, nutrient turnover rate and ecosystem stability by altering soil pH and total carbon (TC). In conclusion, Bacillus sp. T28 combined with sea buckthorn pomace regulated the indigenous soil microbial community structure and mitigated the environmental risk of conventional N fertilization in agroecosystems.

Sugars and Jasmonic Acid Concentration in Root Exudates Affect Maize Rhizosphere Bacterial Communities.

Root exudates contribute to shaping the root-associated microbiomes, but it is unclear which of the many exudate compounds are important in this process. Here, we focused on understanding the influence of sugars and jasmonic acid (JA) concentrations in maize root exudates on the rhizobacterial communities. Twelve maize genotypes were identified with variable concentrations of sugars and JA based on a screening of 240 maize genotypes grown in a semihydroponic system. These twelve maize genotypes were grown in a replicated field experiment in which samples were collected at three maize developmental stages. The 16S rRNA gene (V4 region) was amplified and sequenced. Sugars and JA concentrations from rhizosphere soils were also quantified. The results indicated that the maize genotypic variability in sugars and JA concentration in root exudates, measured in the semihydroponic system, significantly affected the rhizosphere bacterial community composition at multiple stages plant development. In contrast, the root endosphere and bulk soil bacterial communities were only affected at specific growth stages. Sugars and JA concentration as quantified in rhizosphere soil samples confirmed that these two compounds affected the rhizobacterial communities at all developmental stages analyzed. The effects of specific sugars on the composition of the rhizobacterial communities were also measured, with larger effects of sucrose at earlier developmental stages and trehalose at later developmental stages. Our results indicate that JA and sugars are important root exudate compounds that influence the composition of the maize rhizobacterial communities. IMPORTANCE Roots secrete exudates that are important in interactions with soil microbes that promote plant growth and health. However, the exact chemical compounds in root exudates that participate in these interactions are not fully known. Here, we investigated whether sugars and the phytohormone jasmonic acid influence the composition of the rhizobacterial communities of maize, which is an important crop for food, feed, and energy. Our results revealed that both compounds contribute to the assemblage of rhizobacterial communities at different maize developmental stages. Knowledge about the specific compounds in root exudates that contribute to shape the rhizobiome will be important for future strategies to develop sustainable agricultural practices that are less dependent on agrochemicals.

Inoculation with Native Actinobacteria May Improve Desert Plant Growth and Survival with Potential Use for Restoration Practices.

Soil microorganisms, together with water, play a key role in arid ecosystems, being responsible for the nutrient cycle, facilitating nutrient incorporation into plants, influencing plant drought tolerance, and enhancing their establishment. Therefore, their use for restoration practices is promising. We tested the potential of native strains of Actinobacteria from Monte Desert as growth promoters of native vegetation, isolating them from two substrates from their habitat (bare soil and leaf-cutting ant refuse dumps). Strains were inoculated into the soil where seedlings of three native plant species (Atriplex lampa, Grindelia chiloensis, Gutierrezia solbrigii) were growing. Seedlings were grown following a full factorial design experiment under greenhouse and field conditions comparing native Actinobacteria effects with a known growth-promoting strain, Streptomyces sp. (BCRU-MM40 GenBank accession number: FJ771041), and control treatments. Seedlings survived greenhouse condition but species survival and growth were different among treatments at field conditions, varying over time. The highest survival was observed in a native soil strain (S20) while the lowest in MM40. The low survival in MM40 and in the other treatments may be explained by the higher herbivory observed in those seedlings compared to control ones, suggesting a higher nutritional status in inoculated plants. Strains from refuse dumps were the best at enhancing seedling growth, while strains from soil were the best at maintaining their survival. Native Actinobacteria studied may increase plant species survival and growth by improving their nutritional status, suggesting their potential to facilitate vegetation establishment and, therefore, being good candidates for restoration practices. Furthermore, plant species respond differently to different strains, highlighting the importance of microorganism diversity for ecosystem functioning.

Fungal community structure and function shifts with atmospheric nitrogen deposition.

Fungal decomposition of soil organic matter depends on soil nitrogen (N) availability. This ecosystem process is being jeopardized by changes in N inputs that have resulted from a tripling of atmospheric N deposition in the last century. Soil fungi are impacted by atmospheric N deposition due to higher N availability, as soils are acidified, or as micronutrients become increasingly limiting. Fungal communities that persist with chronic N deposition may be enriched with traits that enable them to tolerate environmental stress, which may trade-off with traits enabling organic matter decomposition. We hypothesized that fungal communities would respond to N deposition by shifting community composition and functional gene abundances toward those that tolerate stress but are weak decomposers. We sampled soils at seven eastern US hardwood forests where ambient N deposition varied from 3.2 to 12.6 kg N ha-1  year-1 , five of which also have experimental plots where atmospheric N deposition was simulated through fertilizer application treatments (25-50 kg N ha-1  year-1 ). Fungal community and functional responses to fertilizer varied across the ambient N deposition gradient. Fungal biomass and richness increased with simulated N deposition at sites with low ambient deposition and decreased at sites with high ambient deposition. Fungal functional genes involved in hydrolysis of organic matter increased with ambient N deposition while genes involved in oxidation of organic matter decreased. One of four genes involved in generalized abiotic stress tolerance increased with ambient N deposition. In summary, we found that the divergent response to simulated N deposition depended on ambient N deposition levels. Fungal biomass, richness, and oxidative enzyme potential were reduced by N deposition where ambient N deposition was high suggesting fungal communities were pushed beyond an environmental stress threshold. Fungal community structure and function responses to N enrichment depended on ambient N deposition at a regional scale.

Widespread Occurrence of Pesticides in Organically Managed Agricultural Soils-the Ghost of a Conventional Agricultural Past?

Pesticides are applied in large quantities to agroecosystems worldwide. To date, few studies assessed the occurrence of pesticides in organically managed agricultural soils, and it is unresolved whether these pesticide residues affect soil life. We screened 100 fields under organic and conventional management with an analytical method containing 46 pesticides (16 herbicides, 8 herbicide transformation products, 17 fungicides, seven insecticides). Pesticides were found in all sites, including 40 organic fields. The number of pesticide residues was two times and the concentration nine times higher in conventional compared to organic fields. Pesticide number and concentrations significantly decreased with the duration of organic management. Even after 20 years of organic agriculture, up to 16 different pesticide residues were present. Microbial biomass and specifically the abundance of arbuscular mycorrhizal fungi, a widespread group of beneficial plant symbionts, were significantly negatively linked to the amount of pesticide residues in soil. This indicates that pesticide residues, in addition to abiotic factors such as pH, are a key factor determining microbial soil life in agroecosystems. This comprehensive study demonstrates that pesticides are a hidden reality in agricultural soils, and our results suggest that they have harmful effects on beneficial soil life.

Soil microbial functioning and organic carbon storage: can complex timber tree stands mimic natural forests?

Conversion of natural forest to anthropogenic land use systems (LUS) often leads to considerable loss of carbon, however, proper management of these LUS may reverse the trend. A study was conducted in a semi-deciduous forest zone of Côte d'Ivoire to assess soil microbial functioning and soil organic carbon (SOC) stocks in varying tree stands, and to determine whether complex tree stands can mimic the natural forest in terms of these soil attributes. Tree plantations studied were monocultures of teak (Tectona grandis) and full-sun cocoa (Theobroma cacao L.), and a mixture of four tree species (MTS) with Tectona grandis, Gmelina arborea, Terminalia ivoriensis and Terminalia superba. An adjacent natural forest was considered as the reference. Each of these LUS had five replicate stands where soil (0-10 cm depth) samples were taken for physico-chemical parameters and microbial biomass-C (MBC), microbial activities, MBC/SOC ratio and metabolic quotient (qCO2). SOC and total N stocks were also calculated. The C mineralization rate (mg C-CO2 kg-1) and mineral N concentration (mg kg-1) drastically declined in the monocultures of cocoa (154.9 ± 29.3 and 49.8 ± 9.8, respectively) and teak (179.6 ± 27.1 and 54.1 ± 7.3) compared to the natural forest (258.4 ± 21.9 and 108.7 ± 12). However, values in MTS (194.7 ± 24.6 and 105.4 ± 7.4) were not significantly different from those in the natural forest. Similarly, SOC stocks in MTS (28.8 ± 1.9 Mg ha-1) were not significantly different from those recorded in the natural forest (32.9 ± 1.7 Mg ha-1) whereas teak (25.4 ± 1.7 Mg ha-1) and cocoa (23.1 ± 3.4 Mg ha-1) exhibited significantly lower values. Despite the acidic soil and recalcitrant litter conditions, increased MBC/SOC ratio and decreased qCO2 were recorded in the monocrops, suggesting a probable increase in the fungi/bacteria ratio. The complex MTS stand was found to mimic the natural forest in terms of soil microbial activity and organic status, due to the provision of a diversity of litter quality, which may serve as a basis for developing a climate smart timber system in West and Central Africa.

Contrasting Patterns of Functional Diversity in Coffee Root Fungal Communities Associated with Organic and Conventionally Managed Fields.

The structure and function of fungal communities in the coffee rhizosphere are influenced by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities under markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic, or transitional management in two regions of Costa Rica. We amplified the internal transcribed spacer 2 (ITS2) region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, and more leaf litter and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium availability than conventionally managed fields, although differences between organic and conventionally managed fields in shade and calcium and magnesium availability depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally managed fields were also correlated with shade, soil acidity, and nitrate and copper availability. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse, and plant pathogens were more abundant, in organic than in conventionally managed fields, while saprotroph-plant pathogens were more abundant in conventionally managed fields. These differences reflected environmental differences and depended on region.IMPORTANCE Rhizosphere fungi play key roles in ecosystems as nutrient cyclers, pathogens, and mutualists, yet little is currently known about which environmental factors and how agricultural management may influence rhizosphere fungal communities and their functional diversity. This field study of the coffee agroecosystem suggests that organic management not only fosters a greater overall diversity of fungi, but it also maintains a greater richness of saprotrophic, plant-pathogenic, and mycoparasitic fungi that has implications for the efficiency of nutrient cycling and regulation of plant pathogen populations in agricultural systems. As well as influencing community composition and richness of rhizosphere fungi, shade management and use of fungicides and synthetic fertilizers altered the trophic structure of the coffee agroecosystem.

Diversity of entomopathogenic fungi associated with Mediterranean fruit fly (Ceratitis capitata (Diptera: Tephritidae)) in Moroccan Argan forests and nearby area: impact of soil factors on their distribution.

BACKGROUND: Studying the ecology of biocontrol-agents is a prerequisite to effectively control medfly (Ceratitis capitata (Diptera: Tephritidae)) with entomopathogenic fungi. In this context, factors affecting the occurrence and distribution of medfly-associated entomopathogenic-fungi were studied. Soil samples (22) were collected from natural and cultivated areas of Souss-region Morocco. RESULTS: A total of 260 fungal isolates belonging to 22 species and 10 genera were obtained by using medfly pupae as bait. Medfly-associated fungi were detected in all studied soils and pupae infection percentages ranged from 3.33% to 48%. Two genera, Fusarium and Beauveria were the most frequent with 83 isolates (32%) and 50 isolates (19.23%) respectively. Pathogenicity test of isolated species against medfly pupae showed high mortality rates up to 91% for some strains. Principal component analysis (PCA) demonstrated a strong influence of origin, physical, and chemical properties of soil on the abundance of these fungi. In general, medfly-associated fungi were more abundant in soils with moderate pH (7.5 to 8) having high sand and organic content. High relative humidity negatively influenced the abundance of these fungi. Both factors directly affected the fungal infection percentages in pupae. The response of fungi to these parameters varied among species. According to principal component analysis (PCA), the soils of argan fields and forests were more suitable for the development of medfly-associated fungi than citrus orchards. CONCLUSIONS: These results guide identifying suitable soils for the effective application of entomopathogenic fungi as biological control agents. In summary, isolated indigenous strains seem to be a promising option to control C. capitata.

Nematodes and the effect of seasonality in grassland habitats of South Africa.

Nematodes in South Africa have mainly been studied for their diversity and agricultural importance. However, the ecological status of nematodes and the effect of seasonal variation in local grasslands remain unknown. For this reason, a nematode study was conducted in the Telperion Nature Reserve and represented the first ecological study in a natural grassland area in South Africa. In total, 104 soil samples were collected during four consecutive seasons from 2015 until 2016 in three habitats, viz. (i) open grassland, (ii) shrubland with rocky outcrops, and (iii) riparian zone. From these the nematode community structure and soil ecosystem status were studied. In total, 93 genera from 50 families were recorded with herbivores and bacterivores being the most abundant trophic groups in all three habitats. Linear mixed models revealed that season had an overwhelmingly dominant impact on the condition, food web status, and functioning of the soil ecosystems with pairwise comparisons indicating that significantly higher values were recorded during winter. Interestingly, this seasonal shift can largely be attributed to fluctuations in the populations of only a few nematode groups (namely Aporcelaimellus, Dorylaimidae, Iotonchus, and Mononchus) with high colonizer-persister values. Although the reason for the higher abundance of specific nematode groups recorded during the winter is not explicitly clear, it is possibly linked to reduced competition from other soil fauna. This study clearly shows that further investigations are required to better understand the dynamics of grassland ecosystems.

Volatile emissions from thawing permafrost soils are influenced by meltwater drainage conditions.

Vast amounts of carbon are bound in both active layer and permafrost soils in the Arctic. As a consequence of climate warming, the depth of the active layer is increasing in size and permafrost soils are thawing. We hypothesize that pulses of biogenic volatile organic compounds are released from the near-surface active layer during spring, and during late summer season from thawing permafrost, while the subsequent biogeochemical processes occurring in thawed soils also lead to emissions. Biogenic volatile organic compounds are reactive gases that have both negative and positive climate forcing impacts when introduced to the Arctic atmosphere, and the knowledge of their emission magnitude and pattern is necessary to construct reliable climate models. However, it is unclear how different ecosystems and environmental factors such as drainage conditions upon permafrost thaw affect the emission and compound composition. Here we show that incubations of frozen B horizon of the active layer and permafrost soils collected from a High Arctic heath and fen release a range of biogenic volatile organic compounds upon thaw and during subsequent incubation experiments at temperatures of 10°C and 20°C. Meltwater drainage in the fen soils increased emission rates nine times, while having no effect in the drier heath soils. Emissions generally increased with temperature, and emission profiles for the fen soils were dominated by benzenoids and alkanes, while benzenoids, ketones, and alcohols dominated in heath soils. Our results emphasize that future changes affecting the drainage conditions of the Arctic tundra will have a large influence on volatile emissions from thawing permafrost soils - particularly in wetland/fen areas.

Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.).

Phosphate is a macronutrient and often the limiting growing factor of many ecosystems. The aim of this work was to assess the effect of various phosphate sources on the active bacterial microbiota of barley rhizosphere and endorhiza. Barley was grown on poor soil supplemented with either Ca(H2PO4)2 (CaP), Gafsa rock phosphate (Gafsa), sodium hexaphytate (NaHex), or not amended (P0). RNA was extracted and cDNA synthesized via reverse transcription from both rhizosphere and endorhiza of barley roots; the obtained 16S rRNA cDNA was sequenced by Ion Torrent and analyzed with QIIME and co-occurrence network analysis. Phosphatase activity was measured in the rhizosphere. The phosphate source significantly affected alpha- and beta-diversities of the active microbiota, especially in the rhizosphere. CaP enriched the relative abundance of a broad range of taxa, while NaHex and Gafsa specifically enriched one dominant Massilia-related OTU. Co-occurrence network analysis showed that the most abundant OTUs were affected by phosphate source and, at the same time, were low connected to other OTUs (thus they were relatively "independent" from other bacteria); this indicates a successful adaptation to the specific abiotic conditions. In the rhizosphere, the phosphatase activities were correlated to several OTUs. Moreover, the phosphodiesterase/alk. phosphomonoesterase ratio was highly correlated to the dominance index of the microbiota and to the relative abundance of the dominant Massilia OTU. This study shows the differential response of the rhizosphere- and endorhiza bacterial microbiota of barley to various phosphate sources in soil, thus providing insights onto this largely unknown aspect of the soil microbiome ecology and plant-microbe interactions.

Positive diversity-functioning relationships in model communities of methanotrophic bacteria.

Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH4 at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH4 consumption and community size were positively correlated. The temporal CH4 consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.

Exploration, antifungal and antiaflatoxigenic activity of halophilic bacteria communities from saline soils of Howze-Soltan playa in Iran.

In the present study, halophilic bacteria communities were explored in saline soils of Howze-Soltan playa in Iran with special attention to their biological activity against an aflatoxigenic Aspergillus parasiticus NRRL 2999. Halophilic bacteria were isolated from a total of 20 saline soils using specific culture media and identified by 16S rRNA sequencing in neighbor-joining tree analysis. Antifungal and antiaflatoxigenic activities of the bacteria were screened by a nor-mutant A. parasiticus NRRL 2999 using visual agar plate assay and confirmed by high-performance liquid chromatography. Among a total of 177 halophilic bacteria belonging to 11 genera, 121 isolates (68.3%) inhibited A. parasiticus growth and/or aflatoxin production. The most potent inhibitory bacteria of the genera Bacillus, Paenibacillus and Staphylococcus were distributed in three main phylogenetic clusters as evidenced by 16S rRNA sequence analysis. A. parasiticus growth was inhibited by 0.7-92.7%, while AFB1 and AFG1 productions were suppressed by 15.1-98.9 and 57.0-99.6%, respectively. Taken together, halophilic bacteria identified in this study may be considered as potential sources of novel bioactive metabolites as well as promising candidates to develop new biocontrol agents for managing toxigenic fungi growth and subsequent aflatoxin contamination of food and feed in practice.

Predictors of Arbuscular Mycorrhizal Fungal Communities in the Brazilian Tropical Dry Forest.

Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi with a broad distribution, and many taxa have physiological and ecological adaptations to specific environments, including semiarid ecosystems. Our aim was to address regional distribution patterns of AMF communities in such semiarid environments based on spore morphological techniques. We assessed AMF spores at the bottom and top of inselbergs distributed throughout the tropical dry forest in the Northeast region of Brazil. Across 10 replicate inselbergs and the surrounding area, spanning a range of altitude between 140 and 2000 m, we scored the AMF soil diversity and properties in 52 plots. We fitted parsimonious ordination analyses and variance partitioning models to determine the environmental factors which explained the variation in AMF community, based on morphological spore analysis. The diversity of AMF was similar at the bottom and top of inselbergs; however, we detected high variation in abundance and richness across sites. We formulated a parsimonious richness model that used physical soil factors as predictors. The AMF community structure could be best explained through the variables coarse and total sand, iron, organic matter, potassium, silt, and sodium which together accounted for 17.8% of total variance. Several AMF species were indicators of either deficiency or high values of specific soil properties. We demonstrated that habitat isolation of the inselbergs compared with surrounding areas did not trigger differences in AMF communities in semiarid regions of Brazil. At the regional scale, soil predictors across sites drove the distribution of symbiotic mycorrhizal fungi.

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe.

Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of faster-growing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities.

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the ß-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function.