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Highlights 1. Biochar amendment impeded methanogenesis and facilitated methane oxidation whereas dung amendment facilitated methanogenesis and impeded methane oxidation in grassland soils. 2. Dung amendment generated undominated processes rather than homogeneous selection as the primary driving force in the community assembly of methanogen. 3. Biochar amendment raised the contribution of dispersal limitation in the community assembly of methanotrophs. 4. Diversity and association of the network among the functional genes involved in carbon and nitrogen cycling decreased after biochar and dung amendments.

Understanding the distribution and abundance of microbial stress-related genes (SRGs) is crucial for unraveling the intricate dynamics of microbial communities and their responses to diverse environmental conditions. Despite the importance of these genes in shaping microbial adaptation and resilience, a comprehensive examination of their relative abundance across distinct climatic regions, such as boreal, temperate, and tropical environments, remains notably scarce in the existing literature. This study seeks to address this research gap by exploring and comparing the relative abundances of microbial SRGs using GeoChip 5.0 functional gene array in these three climatic regions. Our data indicate a greater relative abundance of SRGs such as nsrR , degP , cpxR, ahpF , Obg and cisD in the tropical region than in the other two regions whereas ecf and glnA showed higher abundance in both temperate and tropical regions in terms of reference forests and old parks. The distinct characteristics of the tropical biome are likely to influence both SRGs and the profile of SRG-hosts, consequently enhancing soil microbial abundances. Moreover, multivariate analyses unveiled distinct SRG profiles in urban parks and climatic regions. Additionally, we explored the influence of plant functional types (recalcitrant and labile tree litter, lawn) on SRGs. The impact of vegetation type on SRGs was not statistically significant, except in the tropical region, where its influence was notably pronounced compared to the boreal and temperate regions. Furthermore, several genes (nsrR , degP , cpxR , degS , dnaK , Obg , cisD , and glnA) were more prevalent in old parks when compared to young parks in all three climatic regions. However, urban parks displayed a significantly elevated abundance of SRGs compared to forest areas. This study provides new insights into the prevalence of SRGs across different climatic regions, enhancing our understanding of their dynamics in both human-influenced environments and pristine habitats. [Display omitted] [ABSTRACT FROM AUTHOR]

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p

The 2010 Deepwater Horizon disaster remains one of the largest oil spills in history. This event caused significant damage to coastal ecosystems, the full extent of which has yet to be fully determined. Crude oil contains toxic heavy metals and substances such as polycyclic aromatic hydrocarbons that are detrimental to some microbial species and may be used as food and energy resources by others. As a result, oil spills have the potential to cause significant shifts in microbial communities. This study assessed the impact of oil contamination on the function of endophytic microbial communities associated with saltmarsh cordgrass (Spartina alterniflora). Soil samples were collected from two locations in coastal Louisiana, USA: one severely affected by the Deepwater Horizon oil spill and one relatively unaffected location. Spartina alterniflora seedlings were grown in both soil samples in greenhouses, and GeoChip 5.0 was used to evaluate the endophytic microbial metatranscriptome shifts in response to host plant oil exposure. Oil exposure was associated with significant shifts in microbial gene expression in functional categories related to carbon cycling, virulence, metal homeostasis, organic remediation, and phosphorus utilization. Notably, significant increases in expression were observed in genes related to metal detoxification with the exception of chromium, and both significant increases and decreases in expression were observed in functional gene subcategories related to hydrocarbon metabolism. These findings show that host oil exposure elicits multiple changes in gene expression from their endophytic microbial communities, producing effects that may potentially impact host plant fitness. [ABSTRACT FROM AUTHOR]

Thelephora ganbajun is a wild edible mushroom highly appreciated throughout China. The microbiomes of some fungal sporocarps have been studied, however, their potential functional roles currently remain uncharacterized. Here, functional gene microarrays (GeoChip 5.0) and amplicon sequencing were employed to define the taxonomic and functional attributes within three micro-niches of T. ganbajun. The diversity and composition of bacterial taxa and their functional genes differed significantly (p < 0.01) among the compartments. Among 31,117 functional genes detected, some were exclusively recorded in one sporocarp compartment: 1,334 genes involved in carbon (mdh) and nitrogen fixation (nifH) in the context; 524 genes influencing carbon (apu) and sulfite reduction (dsrB, dsra) in the hymenophore; and 255 genes involved in sulfur oxidation (soxB and soxC) and polyphosphate degradation (ppx) in the pileipellis. These results shed light on a previously unknown microbiome and functional gene partitioning in sporome compartments of Basidiomycota. This also has great implications for their potential ecological and biogeochemical functions, demonstrating a higher genomic complexity than previously thought.

Thelephora ganbajun is a wild edible mushroom highly appreciated throughout China. The microbiomes of some fungal sporocarps have been studied, however, their potential functional roles currently remain uncharacterized. Here, functional gene microarrays (GeoChip 5.0) and amplicon sequencing were employed to define the taxonomic and functional attributes within three micro-niches of T. ganbajun. The diversity and composition of bacterial taxa and their functional genes differed significantly (p < 0.01) among the compartments. Among 31,117 functional genes detected, some were exclusively recorded in one sporocarp compartment: 1,334 genes involved in carbon (mdh) and nitrogen fixation (nifH) in the context; 524 genes influencing carbon (apu) and sulfite reduction (dsrB , dsra) in the hymenophore; and 255 genes involved in sulfur oxidation (soxB and soxC) and polyphosphate degradation (ppx) in the pileipellis. These results shed light on a previously unknown microbiome and functional gene partitioning in sporome compartments of Basidiomycota. This also has great implications for their potential ecological and biogeochemical functions, demonstrating a higher genomic complexity than previously thought. [ABSTRACT FROM AUTHOR]

Global nitrogen (N) deposition has a significant impact on the structure and function of above-ground plant communities; however, the impact of N enrichment on below-ground microbial communities remains insufficiently elucidated, especially regarding the functional gene structure. An 18-month pot experiment was conducted to examine the effects of N addition rate (0, 5, 10, and 15 g N m−2 yr−1) on the functional gene composition of rhizosphere microorganisms of Bothriochloa ischaemum , a native grass species of the semiarid area, and to evaluate the soil and plant variables connected with the observed variation. Using microarray GeoChip analysis, 2676, 744, 308, and 515 gene probes involved in carbon (C), N, phosphorus (P) and sulfur (S) cycling, respectively, were detected. Compared with the weak response of genes in the bulk soil, N addition significantly increased the abundance of genes involved in C fixation (tkta , rubisco , TIM), C degradation (amyA , ara , chitinase), methanogenesis (mcra), N 2 -fixation (nifH), denitrification (narG , nirK/S , nosZ), polyphosphate degradation (ppx), and sulfite reduction (dsrA , dsrB , cysJ) in the rhizosphere. The abundance of genes responsible for C-, N-, P-, and S-cycling increased with the N addition rate and was mainly regulated by variations in plant biomass and root exudates. The quantity of soil dissolved organic C played a crucial role in determining the abundance of genes related to the cycling of C, N, P, and S. Plant biomass indirectly affected gene abundance by increasing organic acids in root exudates and dissolved organic C. These findings facilitate our understanding of microbial function to elevated N levels and highlight the key role of root exudates and plant biomass in regulating microbial functions under future N-enrichment scenarios. [Display omitted] • The C, N, P, and S cycling gene abundance increases with the N addition rate. • Increased N deposition would accelerate biogeocycling in semi-arid grassland. • The functional gene abundance was mainly regulated by plant biomass and root exudates. • Soil dissolved organic C plays a crucial role in determining gene abundance. [ABSTRACT FROM AUTHOR]

• Elevated temperature in acidogenesis reactor enhanced the phase separation. • Elevated temperature increased abundance of carbon degradation functional genes. • Influent characteristics and operational conditions explained most of the variance. A robust microbial community is essential for the overall stability and performance of the anaerobic digestion process. In this study, two digesters of a full-scale temperature-phased anaerobic digestion plant treating waste activated sludge were sampled for one year. The acidogenesis reactor (AR) was run at 45 ± 2 °C for six months in Period I and was run at 38 ± 2 °C for six months in Period II. While the methanogenesis reactor (MR) was run at 36 ± 3 °C throughout the year. 16S rRNA amplicon sequencing and GeoChip 5.0 results showed that samples were clearly differentiated by reactors and periods. The elevated temperature in AR during Period I improved the effects of phase separation between the AR and MR. In AR, Fervidobacterium , assigned to Class Thermotogae , had a higher relative abundance of 8.9% in Period I. The abundance of genes involved with carbon degradation was significantly higher in Period I than Period II. In MR, the relative abundance of Methanosarcina increased from 19.8% in Period I to 30.6% in Period II. In addition, the influent characteristics, reactor performance, and operating parameters were determined as the key variables shaping the microbial community, contributing to a total of 76.3% and 69.5% of the variance of the AR and MR, respectively. Combined, this study enriches our understanding of genomic dynamics in full scale temperature-phased anaerobic digestion process. [ABSTRACT FROM AUTHOR]

To address the global concern of antibiotic resistance, a one-health concept is considered necessary that recognizes the interdependency between humans, animals and the environment, and acknowledges that each of these factors contributes to the evolution and rapid bloom of antibiotic resistance genes (ARGs). We implemented a GeoChip 5.0 strategy to examine the wide-spectrum profile of ARGs in the soil of urban parks and reference forests across three distinct climatic regions: Boreal (Lathi, Finland), Temperate (Baltimore, USA), and Tropical (Singapore). ARGs encoding multidrug resistance (MRGs) were among the most abundant, accounting for 90% of all ARGs detected. MRGs include MFS , MATE , Mex , SMR and ABC , which are involved in the transportation/efflux of multiple antibiotics. Multivariate analysis revealed that the ARG profile tends to be partitioned separately in urban parks and climatic regions. In addition, we opted to examine the impact of plant functional type (recalcitrant and labile tree litter, lawn) on ARGs. There was no significant influence of vegetation type on ARGs except in the tropical region, where its impact was evident as compared with boreal and temperate regions. More interestingly, the majority of ARGs were detected to have a higher relative abundance in the tropical region as compared to the boreal and temperate regions. Regional characteristics of the tropical area likely affects ARGs and the ARG-host profile, thereby boosting soil microbial abundances. Additionally, MFS, Mex, B_lactamase_A, vgb, ABC, Van, fosb, ABC_ multi, Tet and Mate_antibiotic were considerably more abundant in old parks as compared with young parks across the three climatic regions. Nevertheless, urban parks harboured a significantly higher abundance of ARGs than forests. Our study presents evidence of ARGs in varied climatic regions and provides valuable new insights in our understanding of ARGs in human-dominated environments as well as their prevalence in pristine ecosystems. [Display omitted] [ABSTRACT FROM AUTHOR]

Although the taxonomical/phylogenetic diversity of microbial communities in biological heap leaching systems has been investigated, the diversity of functional genes was still unclear, and, especially, the differentiation and the relationships of diversity and functions of microbial communities in leaching heap (LH) and leaching solution (LS) were also still unclear. In our study, a functional gene array (GeoChip 5.0) was employed to investigate the functional gene diversity, and 16S rRNA gene sequencing was used to explore the taxonomical/phylogenetic diversity of microbial communities in LH and LS subsystems of Dexing copper mine (Jiangxi, China). Detrended correspondence analysis (DCA) showed that both functional gene structure and taxonomical/phylogenetic structure of microbial communities were significantly different between LH and LS. Signal intensities of genes, including genes for sulfur oxidation (e.g., soxB), metal homeostasis (e.g., arsm), carbon fixation (e.g., rubisco), polyphosphate degradation (e.g., ppk), and organic remediation (e.g., hydrocarbons) were significantly higher in LH, while signal intensities of genes for carbon degradation (e.g., amyA), polyphosphate synthesis (e.g., ppx), and sulfur reduction (e.g., dsrA) were significantly higher in LS. Further inspection revealed that microbial communities in LS and LH were dominated by Acidithiobacillus and Leptospirillum. However, rare species were relatively higher abundant in LH. Additionally, diversity index of functional genes was significantly different in LS (9.915 ± 0.074) and LH (9.781 ± 0.165), and the taxonomical/phylogenetic diversity index was also significantly different in LH (4.398 ± 0.508) and LS (3.014 ± 0.707). Functional tests, including sulfur-oxidizing ability, iron-oxidizing ability, and pyrite bioleaching ability, showed that all abilities of microbial communities were significantly stronger in LH than those in LS. Further studies found that most key genes (e.g., soxC and dsrA), rather than functional gene diversity index, were significantly correlated with abilities of microbial communities by linear regression analysis and Pearson correlation tests. In addition, the abilities were significantly correlated with taxonomical/phylogenetic diversity index and some rare species (e.g., Ferrithrix). [ABSTRACT FROM AUTHOR]

Microbial communities play a very important role in soil ecological processes by regulating biogeochemical cycles during biological soil crust (BSC) succession in desert ecosystems. Although the relationships between microbial carbon or nitrogen and the BSC at different successional stages have been a source of great concern, there are few reports regarding the phosphorus (P) and sulfur (S) cycles. In this study, we used a functional gene array (GeoChip 5.0) to analyze the characteristics of microbial communities and their functional genes involved in the P and S cycles along a chronosequence of BSC succession in the Tengger Desert, China. The results showed that the functional genes associated with polyphosphate degradation and sulfite reduction were the major components involved in the P and S cycles, respectively, and the intensities of the functional genes expression involved in the P and S cycles increased significantly in 61-year-old BSCs. Compared with the fungal and archaeal communities, the bacterial community was the major contributor to the P and S cycles, and Proteobacteria (mainly Alphaproteobacteria, Gammaproteobacteria, and Betaproteobacteria) and Actinobacteria were the dominant phyla. A redundancy analysis showed that there was significant synergy between the improvement in soil properties (e.g., soil nutrient content) and the intensities of genes expression related to P and S cycles. These findings indicated that after 61 years, BSC significantly promoted the microbial metabolic potential for P and S cycling, which in turn promoted soil rehabilitation in a desertified dryland. • Polyphosphate degradation and sulfite reduction were the major metabolism processes involved in the P and S cycles in BSCs. • The intensity of gene expression involved in P and S cycles increased significantly in 61-year-old BSC. • Bacterial community was the major contributor to the P and S cycles of BSCs compared to fungi and archaea. [ABSTRACT FROM AUTHOR]

A six-year (2010–2015) study of sugarcane (Saccharum officinarum) and soybean (Glycine max) intercropping combined with reduced nitrogen (N) fertilizer input was conducted to investigate sustainable agriculture via the functional soil microbial community in Southern China. The Illumina MiSeq platform and the microarray GeoChip 5.0 were applied in this study to detect the abundance, diversity and structure of bacterial and fungal communities, and to link specific functional genes with soil microbial-mediated N-cycling processes under experimental practice. The results revealed the α-diversity of bacterial communities to be relatively stable while the fungal α-diversity increased over the years. Intercropped sugarcane on rhizosphere soils under reduced and conventional N input harbor different bacterial and fungal community structures. Specifically, fungal α-diversity (e.g. Ascomycota and Basidiomycota) was found to be more sensitive to field practices while bacterial community (e.g. Bacteroidetes and Acidobacteria) changed moderately in abundance. Besides that, soil TN, AP, pH, and C/N ratio could explain the major variations in structure of soil microbial groups and in key functional genes. This study revealed the effect of N reduction and cropping patterns on functional traits based on both taxa and gene categories of microbial community, thereby improving understanding of structure-function relationships of microbial N-cycling processes in the different N input levels combined with cropping systems. [Display omitted] ● Alpha-diversity of bacterial and functional genes were relatively stable while the fungal α-diversity increased with years. ● Composition of microbial community and functional gene were changed over the experimental duration. ● Rhizospheric soil harboring different microbial communities and gene structures under different N input levels. ● Taxa and gene structures linked to soil N cycling processes based on functional traits. [ABSTRACT FROM AUTHOR]

Agricultural soil is the most important carbon (C) pool on the Earth's surface and is also a source or sink of greenhouse gases. The C cycle is one of the important biogeochemical processes in the agroecosystem and requires microorganisms to participate in many of the important C cycling pathways, such as C fixation, C degradation, and methane metabolism. Insight into the functions of microbial communities in the C cycle can provide a better understanding of the response and feedback of soil microbes with respect to global climate change. The microarray GeoChip 5.0 was used in this study to detect the specific genes linking C cycling and soil microbial-mediated processes and to evaluate the abundance, diversity and similarity of the detected genes responding to different nitrogen (N) application levels under intercropping treatment. Our results indicated that compositional changes in soil microbial communities elicited by N input have functional implications for C cycling and storage in agroecosystems. We further identified a sugarcane (Saccharum officinarum) field as a C sink in this intercropping system, in which sugarcane/soybean (Glycine max) (1:2) strip intercropping (SB2) at the N1 application rate (SB2-N1) had the largest C sequestration potential and net C balance among all the treatments. Most of the functional genes involved in C cycling with regards to fixation and degradation were separately identified after 4 years of N fertilization and intercropping treatments, and environmental factors were central in shaping the functional gene structure related to the C cycles. Overall, our results suggested that reduced N application combined with intercropping treatment mediates ecosystem functions and may have profound feedback effects on global climate change. • Reduced nitrogen fertilizer application improved carbon storage and cycling in the intercropping system • The functional genes or enzymes related to carbon cycle were widely detected in many important carbon cycling pathways • Carbon cycling functional gene structure were shaped by environmental variances • Sugarcane field function as a carbon sink in this intercropping system [ABSTRACT FROM AUTHOR]

To examine soil microbial functional gene diversity and causative factors in tropical rainforests, we used a microarray-based metagenomic tool named GeoChip 5.0 to profile it. We found that high microbial functional gene diversity and different soil microbial metabolic potential for biogeochemical processes were considered to exist in tropical rainforest. Soil available nitrogen was the most associated with soil microbial functional gene structure. Here, we mainly describe the experiment design, the data processing, and soil biogeochemical analyses attached to the study in details, which could be published on BMC microbiology Journal in 2015, whose raw data have been deposited in NCBI's Gene Expression Omnibus (accession number GSE69171).