Microbial Community Functional Structure Research Articles

Enhancing phosphorus bioavailability in lateritic red soil: Combining Bacillus subtilis inoculated microbial organic fertilizer with reduced chemical input

AbstractOptimal phosphorus (P) levels in lateritic soils are key for sustainable crop production. However, the effect of various fertilizers on soil phosphorus pools, crop phosphorus uptake and crop yields remains unclear. This study investigated the effect of different fertilizer application strategies on plant growth and soil P fractions and determined the contribution of biotic and abiotic factors to insoluble P release. We found that resin‐P, NaHCO3‐P and NaOH‐P represented the primary active P pools in the lateritic soil, contributing 59.8% of the total P in conventional fertilizer application (CF), with Fe/Al‐bound P (NaOH‐P) being 42.1% of the active P pool. Combining Nangbowang (NBW), a microbial organic fertilizer inoculated with Bacillus subtilis (≥2 × 107 million CFU g−1), with reduced chemical fertilizer (NBW + CR) increased soil P availability and promoted the release of Fe/Al‐bound P and residual‐P, decreasing the Fe/Al‐bound P to 21.7%. Soil biological factors mainly influenced the P transformation process. With the consumption of soil active P, NBW bio‐organic fertilizer enhanced the niche filtration of P‐solubilizing bacterial communities (Gemmatimonadetes, Sphingomonas and Halomonas), altered the soil functional microbial community structure and promoted P form conversion. The NBW + CR treatment also enhanced nitrogen and P nutrient uptake by pepper plants (Capsicum annuum), with increased total P concentrations in pepper fruit and stem, and improved crop yield. NBW increased active P concentrations in the soil and promoted Fe/Al‐P release and transformation by impacting autochthonous microbes involved in the conversion of P chemical species. These results can guide the improvement of P availability and release in lateritic red soils using bio‐organic fertilizer.

Co-incorporation of Chinese milk vetch (Astragalus sinicus L.) and chemical fertilizer alters microbial functional genes supporting short-time scale positive nitrogen priming effects in paddy soils

Nitrogen (N) priming is a microbially mediated biochemical process as affected by different incorporation practices. However, little information is known about the driving microbial mechanisms behind the response of N priming to co-operation of Chinese milk vetch (Astragalus sinicus L., CMV) and different rates of chemical fertilizers in paddy soils in south China. Here, an anaerobic incubation experiment was conducted to study N priming effects (PE) and their relationships with soil microbial functional genes after the CMV incorporation alone (M), co-incorporation of CMV combined with 100% chemical fertilizers (MC100) and with 80% chemical fertilizers (MC80). Co-incorporation of CMV and chemical fertilizers enhanced the short-time scale (the first 20 days) positive PE of N, while no significant differences existed among the three treatments on day 60 or 90 of incubation (P > 0.05). Compared with the M treatment, gross priming effect (GPE) in the MC100 and MC80 treatments significantly increased by 34.0% and 31.3%, net priming effect (NPE) increased by 47.7% and 47.8% in the first 20 days (P < 0.05). This was likely attributed to soil nutrient availability and added substrate quality. The MC100 and MC80 treatments increased the gdhA abundance by 5.0% and 9.8%, increased the gdh2 gene by 12.7% and 45.7%, and increased the nasB gene by 9.5% and 41.4%, respectively, in comparison with those in the M treatment on day 20 of incubation. Correlation analyses indicated that soil microbial functional genes involved in N mineralization (gdhA and gdh2), assimilatory nitrate reduction (nasB), and nitrification (amoB) were significantly correlated with N priming under different incorporation practices and incubation times (P < 0.05). Thus, co-incorporation of CMV and chemical fertilizers can regulate soil microbial community functional gene structure, which may accelerate mineralization and assimilatory nitrate reduction and inhibit nitrification, thereby increasing the short-term positive PE of N in the present study.

Effects of Chemical Fertilizer Reduction Substitute with Organic Fertilizer on Soil Functional Microbes and Lemon Yield and Quality

To clarify the effects of non-rhizosphere/rhizosphere soil functional microbes (nitrifiers, denitrifiers, and phosphorus-solubilizing microorganisms) on lemon yield and quality, the lemon fruit and non-rhizosphere/rhizosphere soil were selected as subjects. To explore the correlation between non-rhizosphere/rhizosphere soil functional microbes and lemon yield and quality under a chemical fertilizer reduction substitute with organic fertilizer, traditional fruit quality determination and multiple molecular techniques were used. The results showed that:① 30% chemical fertilizer reduction substitute with organic fertilizer increased the nitrification intensity and phosphatase activity but effectively controlled the denitrifying enzyme activity. ② The chemical fertilizer reduction substitute with organic fertilizer significantly decreased the abundances of nitrifiers and nirS/nirK-harboring denitrifiers and significantly increased the abundances of nosZ-harboring denitrifier and phoD-harboring microorganisms. However, the diversities of functional microbial community structure did not have clear regularity under chemical fertilizer reduction substitute with organic fertilizer. ③ Compared with that under the application of chemical fertilizer and organic fertilizer alone, lemon yield and quality were the highest under the 30% reduction of chemical fertilizer substitute with organic fertilizer. ④ Nitrogen and its related microbes significantly affected lemon yield through internal and external quality. Phosphorus and its related microbes affected lemon yield mainly through internal quality. In addition, the influence factors of non-rhizosphere soil and rhizosphere soil on lemon intrinsic quality were obviously different. Altogether, these results showed that the 30% reduction of chemical fertilizer substitute with organic fertilizer significantly affected soil nitrogen and phosphorus functional microorganisms and further improved lemon yield and quality.

Characterizing a subtropical hypereutrophic lake: From physicochemical variables to shotgun metagenomic data.

Lake Cajititlán is a subtropical and endorheic lake, which is heavily impacted by nutrient pollution. Agricultural runoff and poorly treated wastewater have entered this reservoir at alarming rates during past rainy seasons, causing the cultural eutrophication of this body of water and resulting in several massive fish kill events. In this study, shotgun metagenomic sequencing was used to examine the taxonomic and functional structure of microbial communities in Lake Cajititlán during the rainy season. Several water quality features and their interactions with microbial communities were also assessed to identify the major factors affecting the water quality and biota, specifically fish species. According to current water quality regulations, most of the physicochemical variables analyzed (dissolved oxygen, pH, Secchi disk, NH4 +, NO3 -, blue-green algae, total phosphorus, and chlorophyll-a) were outside of the permissible limits. Planktothrix agardhii and Microcystis aeruginosa were the most abundant phytoplankton species, and the dominant bacterial genera were Pseudomonas, Streptomyces, and Flavobacterium, with Pseudomonas fluorescens, Stenotrophomonas maltophilia, and Aeromonas veronii representing the most abundant bacterial species. All of these microorganisms have been reported to be potentially harmful to fish, and the latter three (P. fluorescens, S. maltophilia, A. veronii) also contain genes associated with pathogenicity in fish mortality (fur, luxS, aer, act, aha, exu, lip, ser). Genetic evidence from the microbial communities analyzed herein reveals that anthropogenic sources of nutrients in the lake altered genes involved in nitrogen, phosphorus, sulfur, and carbon metabolism, mainly at the beginning of the rainy season. These findings suggest that abiotic factors influence the structure of the microbial communities, along with the major biogeochemical cycles of Lake Cajititlán, resulting in temporal variations and an excess of microorganisms that can thrive in high-nutrient and low-oxygen environments. After reviewing the literature, this appears to be the first study that focuses on characterizing the water quality of a subtropical hypereutrophic lake through associations between physicochemical variables and shotgun metagenomic data. In addition, there are few studies that have coupled the metabolism of aquatic ecosystems with nutrient cycles.

Humic Lake Exhibits Higher Microbial Functional Gene Diversity and Weaker Gene Interaction Efficiency than a Common Alkaline Lake.

Simple SummaryThe humic lake represents a special kind of aquatic ecosystem with high humic substances, low irradiance, and a high potential for greenhouse gas emissions. Despite the special environment and biogeochemical processes in humic lake water, knowledge about the underlying microbial-driven functions remains elusive. Here, we studied the compositions and functional gene structures of microbial communities in a humic lake (HL) and a reference weakly alkaline lake (RAL). We found that the high organic matter content in the HL supported higher gene diversity; and, specifically, the carbon and nitrogen fixations, the degradation of various types of carbon, methane oxidation and methanogenesis, ammonification, denitrification, and assimilatory N reduction might be enhanced more in the HL than in the RAL. By contrast, the humic fractions in the HL might reduce microbial metabolic potential for sulfur oxidation and phosphorus degradation. The potential interactions between different functional microorganisms might be down-regulated provided that there were more easily acquired nutrients in the HL. Overall, our results showed the functional gene “landscape” of microbial communities in the surface water of a humic lake, which helps understand the biogeochemical processes and the remediation of organic matter pollution in lacustrine ecosystems.Humic lakes (HLs) are special water bodies (high organic matter content, low pH, and low transparency) that are important sources of major greenhouse gases. The knowledge about microbial functional potentials and the interactions among different genes in HL water has been scarcely understood. In this study, we used 16S rRNA gene sequencing and the GeoChip 5.0 to investigate microbial community compositions and functional gene structures in an HL and a reference weakly alkaline lake (RAL). The HL microbial communities showed distinct compositions and functional gene structures than those in the RAL. The functional gene diversity was significantly higher in the HL than in the RAL. Specifically, higher gene relative intensities in carbon and nitrogen fixations, the degradation of various types of carbon, methane oxidation and methanogenesis, ammonification, denitrification, and assimilatory N reduction were observed in the HL samples. By contrast, the metabolic potentials of microorganisms involved in dissimilatory N reduction, phosphorus degradation, and sulfur oxidation were weaker in the HL than in the RAL. Despite higher functional gene diversity, the interaction efficiency among genes (reflected by network geodesic distance and clustering coefficient) might be reduced in the HL. Different functional microbes may develop less interdependent relationships in acquiring nutrients given the high resource availability in the HL. Overall, the enhanced microbial metabolic potentials and less efficient functional interactions might have great consequences on nutrient cycling and greenhouse gas emissions in the HL ecosystem.

Aspects of the rhizospheric microbiota and their interactions with the soil ecosystem.

Soil microbial communities play a key role in the evolution of the rhizosphere. In addition, proper exploration of these microbial resources represents a promising strategy that guarantees the health and sustainability of all ecosystems connected to the ground. Under the inf luence of environmental conditions, microbial communities can change compositions in terms of abundance and diversity. Beyond the descriptive level, the current orientation of microbial ecology is to link these structures to the functioning of ecosystems; specif ically, to understand the effect of environmental factors on the functional structure of microbial communities in ecosystems. This review focuses on the main interactions between the indigenous soil microf lora and the major constituents of the rhizosphere to understand, on the one hand, how microbial biodiversity can improve plant growth and maintain homeostasis of the rhizospheric ecosystem, on the other hand, how the maintenance and enrichment of plant biodiversity can contribute to the conservation of soil microbial diversity; knowing that these microorganisms are also controlled by the abiotic properties of the soil. Overall, understanding the dynamics of the rhizosphere microbiome is essential for developing innovative strategies in the f ield of protecting and maintaining the proper functioning of the soil ecosystem

A Systematic Review of Terrestrial Plant Invasion Mechanisms Mediated by Microbes and Restoration Implications

Terrestrial invasive plant species continue to wreak havoc on a global economic and ecological scale. With the advent of climate change and pending future catastrophes, the spread of resilient invasive plants will only increase exponentially. Here, the search continues for a better understanding of the below-ground microbially driven mechanisms involved in plant invasion where other above-ground mechanisms have been exhausted. Microbes govern the world around us and interact with every living and non-living facet of the world. To reinforce the important underpinnings of the role of microorganisms in plant invasion, a systematic review of recently published articles was undertaken. Using the ScienceDirect database, five (5) search queries were used to generate 1221 research articles. After a two-step reduction was made based on relevance of the articles, a final total of 59 articles were retrieved. An additional 18 relevant articles were also assessed through the PubMed database for analysis to account for other invasive plants. Thirty-seven (37) invasive species were investigated where soil physiochemical and microbial community structure changes were most prevalent (32% & 39% respectively) while enhanced mutualism, allelopathy and pathogen accumulation were reported less (16%, 10% & 3% respectively). In all invasive species assessed, the impact on plant invasion and inability of the native plants to compete was due to specific microbial associations of the invasive plant or disruption of the soil microbial community. This microbial community shift coincided with changes in physiochemical properties of the soil and the subsequent negative soil feedback for native plants. There is still an expanding potential for the use of biocontrol agents to aid restoration once the underpinnings of biotic resistance and enemy release are understood in a microbial and physiochemical context. The active and functional microbial community structure of the invasive plant rhizosphere and adjacent soil in its native and non-native region can offer a better inference of how they can be controlled using novel-below ground biocontrol methods.

The diversity and metabolic potential of the microbial functional gene associated with Porites pukoensis.

Coral reef ecosystems usually distribute in oligotrophic tropical and subtropical marine environments, but they possess great biodiversity and high productivity. It may attribute to its efficient internal nutrient cycle system. However, the knowledge of functional microbial community structure is still limited. In this study, both functional gene array (Geochip 5.0) and nifH Illumina sequencing were used to profile the overall functional genes and diazotrophic communities associated with coral Porites pukoensis. More than 7500 microbial functional genes were detected from archaea, bacteria, and fungi. Most of these genes are related to the transformation of carbon, nitrogen, sulfur, and phosphorus, providing evidence that microbes in the coral holobiont play important roles in the biogeochemical cycle of coral reef ecosystems. Our results indicated a high diversity of diazotrophs associated with corals. The dominant diazotrophic groups were related to phyla Alphaproteobacteria, Deltaproteobacteria, Cyanobacteria, and Gammaproteobacteria. And the dominant diazotrophic communities were divided into four clusters. They were affiliated with nifH sequences from genera Zymomonas, Halorhodospira, Leptolyngbya, Trichormus, and Desulfovibrio, indicating these groups may play a more important role in the nitrogen-fixing process in the coral holobiont. This study revealed functional gene diversity and suggested the roles they played in the biogeochemical cycling of the coral holobiont.

Organic manure input and straw cover improved the community structure of nitrogen cycle function microorganism driven by water erosion

Water erosion process induces differences to the nitrogen (N) functional microbial community structure, which is the driving force to key N processes at soil-water interface. However, how the soil N transformations associated with water erosion is affected by microorganisms, and how the microbial respond, are still unclear. The objective of this study is to investigate the changes of microbial diversity and community structure of the N-cycle function microorganisms as affected by water erosion under application of organic manure and straw cover. On the basis of iso-nitrogen substitution, four treatments were set up: 1) only chemical fertilizer with N 150 kg ha−1, P2O5 60 kg ha−1 and K2O 90 kg ha−1 (CK); the N was substituted 20% by 2) organic manure (OM); 3) straw (SW); and 4) organic manure + straw (1:1) (OMSW). The results showed that applying organic manure and straw to sloping farmland can increase soil N contents, but reduce runoff depth, Kw, sediment yield and N loss, especially in the OMSW. Straw cover and straw + organic manure increased the diversity (Chao1) of nitrifier (AOB), and both diversity and uniformity (Shannon) of denitrifier (nirK/S) were increased in the OMSW. All erosion control measures reduced N-fixing bacteria diversity and increased their uniformity, and the combined application of organic manure and straw cover was a better erosion control measure than the single application of them. Improved soil chemistry and erodibility were the main drives for the changes of N-functional microbial community structure and the appearance of dominant bacteria with different organic materials.

Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions.

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

Microbiological Approach to Reconstruction of the Original Content of Pots from the Burials

In a model soil experiment, microbial decomposition nature and its rate applying to various organic substrates were studied. It is shown that the decomposition of various materials changes the functional features of microbial communities. These changes are assessed using multisubstrate testing of respiratory activity of microbial communities – this testing assumes application of low- molecular respiratory inducers (aminoacids and carboxylic acids) to the soil and registration the changes of the intensity of carbon dioxide release by microorganisms. Indicative compounds such as ascorbate, lactate, acetate (from the group of carboxylic acid salts) and cysteine (from the group of aminoacids) have been identified to be promising for use in reconstructing the original contents of ritual vessels. As an example, the article presents the results of reconstruction of one of bronze age burial pots original content, obtained by multisubstrate testing. High microbial biomass in the bottom layer of the vessel and the specific microbial communities’ respiratory responses to carboxylic acids salts (ascorbate, lactate and acetate) and aminoacid cysteine addition, indicate that the vessel originally contained a nutritional product, the decomposition of which led both to increase of microbial biomass and to changes in the functional structure of microbial community in the soil filling of the bottom layer. The results of statistical analysis of the reactions of soil microbial communities from the pot and from soils of the model experiment with known materials decomposed indicate that the vessel initially contained a protein product with a possible component of oil and starch.

Microbial community functional structure in an aerobic biofilm reactor: Impact of streptomycin and recovery

Antibiotics can affect microbial community structure and promote antibiotic resistance. However, the course of microbial community recovery in wastewater treatment systems after antibiotic disturbance remains unclear. Herein, multiple molecular biology tools, including 16S amplicon sequencing, GeoChip 5.0, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing, were used to investigate the year-long (352 d) recovery of the microbial community functional structure in an aerobic biofilm reactor. Nitrification was completely inhibited under 50 mg/L of streptomycin spiking (STM_50) due to the significant reduction of ammonia-oxidizing bacteria, but recovered to original pre-disturbance levels after streptomycin removal, indicating the high resilience of ammonia-oxidizing bacteria. Bacterial community richness and diversity decreased significantly under STM_50 (p < 0.05), but recovered to levels similar to those observed before disturbance after 352 d. In contrast, bacterial composition did not recover to the original structure. The carbon degradation and nitrogen cycling functional community significantly changed after recovery compared to that observed pre-disturbance (p < 0.05), thus indicating functional redundancy. Additionally, levels of aminoglycoside and total antibiotic resistance genes under STM_50 (relative abundance, 0.33 and 0.80, respectively) and after one year of recovery (0.12 and 0.29, respectively) were higher than the levels detected pre-disturbance (0.04 and 0.24, respectively). This study provides an overall depiction of the recovery of the microbial community functional structure after antibiotic exposure. Our findings give notice that recovery caused by antibiotic disturbance in the water environment should be taken more seriously, and that engineering control strategies should be implemented to prevent the antibiotic pollution of wastewater.

Spatial and temporal patterns in soil organic carbon, microbial biomass and activity under different land-use types in a long-term soil-monitoring network

Preservation of soil organic carbon (SOC) requires knowledge concerning the quantity and quality of both the SOC and the SOC-decomposing microbial community. In northern Germany, this information is assessed as part of Schleswig-Holstein’s long-term soil-monitoring programme, in which topsoils have been analysed since 1995. In this study, we evaluated long-term data from Schleswig-Holstein’s monitoring sites and compared the content of SOC and microbial biomass carbon (MBC) among croplands, grasslands and forests. We distinguished the microbial fractions as total MBC (chloroform fumigation extraction method) and glucose-responsive MBC, and we used the MBC/SOC ratio and soil basal respiration (SBR) to obtain a qualitative view of the SOC and its turnover potential. Additionally, we performed a temporal comparison for SOC and MBC between the periods 1995–2002 and 2005–2015. The results showed that median SOC content is the highest in forest soils (41 g kg−1), followed by grasslands (33 g kg−1), and croplands (12 g kg−1). Different ascending orders occurred for the total MBC (cropland < forest < grassland), however, and for the glucose-responsive MBC (forest < cropland < grassland), indicating differences in SOC quality and the microbial community structure. The different ratios between MBC and SOC showed that SOC in croplands and grasslands is characterised as easily degradable, but more stable in grasslands under no-till conditions. Forest SOC appears almost non-degradable, and thus is most stable in the long term. We concluded that land-use-specific carbon characteristics, including the functional microbial community structure, are beneficial for evaluation of SOC preservation potential. From the temporal perspective, a significant increase (45–114 %) was observable for the total MBC on cropland and grassland sites, whereas the changes in SOC were not significant. The remarkable growth of the total MBC in relation to the glucose-responsive MBC indicates shifts in the microbial community towards a K-strategy metabolism.

Does electrolysis facilitate simultaneous nitrogen removal and toxicity reduction of low C/N dyeing wastewater by sulfur-based denitrification biofilter?

The concern about wastewater effluent toxicity has motivated the innovation of enhancement technologies on sulfur-based denitrification biofilter in recent years. Electrolysis is a common technology to reduce or remove toxic pollutants. However, the effect of electrolysis on simultaneous total nitrogen (TN) removal and toxicity reduction in sulfur-based denitrification biofilter has not been reported yet. Herein, for the first time, this study investigated the synergistic effects of electrolysis-induced TN removal and toxicity reduction of secondary effluent of dyeing wastewater containing 20 μg/L of nonylphenol (NP), at different carbon to nitrogen ratios (C/N) in several sulfur-based denitrification biofilters. All of the biofilters achieved the denitrification rate of 300.15 g∙N/m3∙d during the stabilization period at C/N = 5. The CSAHD (ceramisite and sulfur as filters) biofilter had highest TN removal rate to achieve the denitrification rate of 257.46 g∙N/m3·d at C/N = 2. Siderite and dolomite both facilitated TN removal efficiency by 9.3%–12.6% under low C/N ratio and acted as the buffer agent in biofilters. Toxicity characteristic leaching procedure (TCLP) test showed that the amount of leached heavy metals was lower than the concentration limit standard of USEPA. Electrolysis did not promote the removal of TN, however, it could reduce NP concentration and increase the biotoxicity relative inhibition rate of effluent by 12.5%–167%, and affect the functional microbial community structure. Our work clarified some misunderstandings about the application of electrolysis-based strengthening technology and enlightened the future development of simultaneous TN removal and toxicity reduction of dyeing wastewater.

Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location.

Previous studies indicate that the plant phenotypic traits eventually shape its microbiota due to the community assembly based on the functional types. If so, the distance-related variations of microbial communities are mostly only in taxonomical composition due to the different seeds pool, and there is no difference in microbial community functional structure if the location associated factors would not cause phenotypical variations in plants. We test this hypothesis by investigating the phyllospheric microbial community from five species of spruce (Picea spp.) trees that planted similarly but at three different locations. Results indicated that the geographical location affected microbial taxonomical compositions and had no effect on the community functional structure. In fact, this actually leads to a spurious difference in the microbial community. Our findings suggest that, within similar host plants, the phyllosphere microbial communities with differing taxonomical compositions might be functionally similar.

Taxonomic and functional responses of soil microbial communities to slag-based fertilizer amendment in rice cropping systems

The effective utilization of slag-based Silicon fertilizer (silicate fertilizer) in agriculture to improve crop productivity and to mitigate environmental consequences turns it into a high value added product in sustainable agriculture. Despite the integral role of soil microbiome in agricultural production and virtually all ecosystem processes, our understanding of the microbial role in ecosystem functions and agricultural productivity in response to the silicate fertilizer amendment is, however, elusive. In this study, using 16S rRNA gene and ITS amplicon illumina sequencing and a functional gene microarray, i.e., GeoChip 5, we report for the first time the responses of soil microbes and their functions to the silicate fertilizer amendment in two different geographic races of Oryza sativa var. Japonica (Japonica rice) and var. Indica (Indica rice). The silicate fertilizer significantly increased soil pH, photosynthesis rate, nutrient (i.e., C, Si, Fe, P) availability and crop productivity, but decreased N availability and CH4 and N2O emissions. Moreover, the silicate fertilizer application significantly altered soil bacterial and fungal community composition and increased abundance of functional genes involved in labile C degradation, C and N fixation, phosphorus utilization, CH4 oxidation, and metal detoxification, whereas those involve in CH4 production and denitrification were decreased. The changes in the taxonomic and functional structure of microbial communities by the silicate fertilizer were mostly regulated by soil pH, plant photosynthesis, and nutrient availability. This study provides novel insights into our understanding of microbial functional processes in response to the silicate fertilizer amendment in rice cropping systems and has important implications for sustainable rice production.

Shifts in soil microbial community functional gene structure across a 61-year desert revegetation chronosequence

Vegetation and soil properties are crucial in shaping soil microbial communities. However, little is known about temporal changes in the functional structure of soil microbial communities to managed revegetation in desert ecosystems. Here, we adopted GeoChip 5.0-180 K, a functional gene array, to investigate the succession of soil microbial functional genes structure and potential across a 61-year revegetation chronosequence in the Tengger Desert, China. The abundance of bacterial, fungal and archaeal genes generally increased during succession. However, variation in α-diversity of microbial functional genes and signal intensity of most C-, N- and P-cycling related genes showed hump-shaped patterns along the successional gradient. Although microbial functional structure changed during succession, these revegetation sites shared a high percentage of functional genes and nestedness-resultant component dominantly determined β-diversity. Furthermore, microbial functional structure significantly correlated with crustal and shrub coverage, thickness and mass of crusts, soil fine particles, total C, total P and the ratios of C to N and C to P. The canonical correspondence analysis (CCA) and CCA-based variation partitioning analysis showed that environmental variables explained 56.6% and 85.3% of the variance in overall microbial functional genes, respectively. These results indicate that vegetation development, especially the colonization and development of soil crusts together with changes in soil abiotic properties, play key roles in driving the functional shifts in soil microbial community structure after desert revegetation.

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.

A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a “resource-limited” regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species’ consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.

Функціональна структура мікробних угруповань чорнозему глибокого за впливу гідротермічних і трофічних чинників

Функціональна структура мікробних угруповань чорнозему глибокого за впливу гідротермічних і трофічних чинників

Process performance and microbial community functional structure in a thermophilic anaerobic baffled reactor coupled with biocatalysed electrolysis

ABSTRACTIn this study, the performances of a conventional anaerobic baffled reactor (ABR) and an ABR combined with microbial electrolysis cells (MECs) for enhancing degradation of volatile fatty acids (VFAs) were evaluated in 55°C. The ABR-MECs system achieved a total chemical oxygen demand (COD) removal rate of 97.2% and a methane yield of 236 ± 5 mL g−1 CODremoved at organic loading rate (OLR) of 6.9 kg COD m−3 d−1, which were higher than those of the ABR with 77.6% and 207 ± 5 mL g−1 CODremoved, respectively, at OLR of 5.1 kg COD m−3 d−1. The pyrosequencing analysis confirmed that the introduction of MECs into ABR was conducive to establishing stable functional communities of syntrophic fatty acids oxidizing bacteria (SFOB), exoelectrogens and hydrogenotrophic methanogens, such as Syntrophobacter (5.4%), Thermodesulfovibrio (2.0%), Methanobacterium (43.8%), Methanolinea (20.4%). The content of unclassified bacteria increased from 12.4% in the ABR system to 52.3% in the ABR-MECs system. In contrast, the proportion of aceticlastic methanogens decreased from 50.1% in the ABR to 24.5% in the ABR-MECs system. The improved performance of the thermophilic ABR-MECs system resulted from phase separation, wide ecological niche and intensification of methanogenesis process via functional microbes, which significantly enhanced the degradation of propionic acid and acetic acid.