Microbial Functional Structure Research Articles

Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems.

The cheese making and vegetable processing industries generate immense volumes of high-nitrogen wastewater that is often treated at rural facilities using land applications. Laboratory incubation results showed denitrification decreased with temperature in industry facility soils but remained high in soils from agricultural sites (75% at 2.1°C). 16S rRNA, phospholipid fatty acid (PLFA), and soil respiration analyses were conducted to investigate potential soil microbiome impacts. Biotic and abiotic system factor correlations showed no clear patterns explaining the divergent denitrification rates. In all three soil types at the phylum level, Actinobacteria, Proteobacteria, and Acidobacteria dominated, whereas at the class level, Nitrososphaeria and Alphaproteobacteria dominated, similar to denitrifying systems such as wetlands, wastewater resource recovery facilities, and wastewater-irrigated agricultural systems. Results show that potential denitrification drivers vary but lay the foundation to develop a better understanding of the key factors regulating denitrification in land application systems and protect local groundwater supplies. PRACTITIONER POINTS: Incubation study denitrification rates decreased as temperatures decreased, potentially leading to groundwater contamination issues during colder months. The three most dominant phyla for all systems are Actinobacteria, Proteobacteria, and Acidobacteria. The dominant class for all systems is Nitrosphaeria (phyla Crenarchaeota). No correlation patterns between denitrification rates and system biotic and abiotic factors were observed that explained system efficiency differences.

Soil ecosystem multifunctionality is strongly linked with crop yield after four decades chemical fertilization in black soil

Soil ecosystem multifunctionality (EMF), the ability of an ecosystem to perform multiple functions, remains uncertain in its contribution to crop production, especially in the context of long-term fertilization ecosystems. This study was carried out on a 40-year-old long-term fertilization experiment in black soil in China. Soil samples were collected from four treatments: control (CK); nitrogen (N) fertilizer; phosphorus (P) fertilizer; and a combination of nitrogen and phosphorus (NP) in both maize and wheat planting seasons. The results showed significant effects of N, P fertilizers and crop season on soil biotic and abiotic properties, especially on soil enzyme activities. Crop productivity and soil EMF showed a similar pattern across different treatments and both crop seasons, with significant higher values recorded in treatments with N addition (i.e. N and NP). Soil EMF was strongly associated with crop productivity in both maize and wheat seasons, while soil pH had a negative impact on crop yield. Random forest analysis revealed that microbial functional gene structure was significantly correlated with both soil ecosystem multifunctionality and crop yield. This suggested that fertilization leads to alterations in soil nutrients and the composition of functional microbial communities, subsequently impacting ecological functions and crop growth. These findings indicated that mineral fertilizers can enhance crop yield through soil EMF in the black soils, while exerted substantial impact on soil properties, raising concerns about the sustainability of soils under continuous chemical fertilization.

Tidal dynamics regulates potential coupling of carbon‑nitrogen‑sulfur cycling microbes in intertidal flats

Tide-driven hydrodynamic process causes significant geochemical gradients that influence biogeochemical cycling and ecological functioning of estuarine and coastal ecosystems. However, the effects of tidal dynamics on microbial communities, particularly at the functional gene level, remain unclear even though microorganisms play critical roles in biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycling. Here, we used 16S rRNA gene amplicon sequencing and microarray-based approach to reveal the stratification of microorganisms related to C, N and S cycles along vertical redox gradients in intertidal wetlands. Alpha-diversity of bacteria and archaea was generally higher at the deep groundwater-sediment interface. Microbial compositions were markedly altered along the sediment profile, and these shifts were largely due to changes in nutrient availability and redox potential. Furthermore, functional genes exhibited redox partitioning between interfaces and transition layer, with abundant genes involved in C decomposition, methanogenesis, heterotrophic denitrification, sulfite reduction and sulfide oxidation existed in the middle anoxic zone. The influence of tidal dynamics on sediment function was highly associated with redox state, sediment texture, and substrates availability, leading to distinct distribution pattern of metabolic coupling of microbes involved in energy flux and elemental cycling in intertidal wetlands. These results indicate that tidal cycles are critical in determining microbial community and functional structure, and they provide new insights into sediment microbe-mediated biogeochemical cycling in intertidal habitats.

Microbial function regulates the effect of vegetation restoration on the contribution of biocrusts to soil respiration in drylands

Abstract Biocrusts are special components of dryland ecosystems and play important roles in ecosystem carbon cycles. Vegetation restoration not only affects carbon storage but also changes the characteristics of biocrusts. However, how vegetation restoration influences the contribution of biocrusts to soil carbon cycling in dryland ecosystems is poorly understood. Using continuous field measurements combined with metagenomic shotgun sequencing, we explored the effect and regulatory mechanisms of Caragana korshinskii vegetation restoration on the contribution of biocrusts to total soil respiration. We found that vegetation restoration increased the contribution of biocrusts to total soil respiration, with the biocrust contribution increasing from −5.6% for mixed biocrusts in a typical steppe to 17.1%, 18.1% and 19.6% for cyanobacteria–algae, lichen and moss biocrusts, respectively, in a Caragana korshinskii vegetation restoration area. The driving factors for total soil respiration changed from solely soil temperature to soil temperature and moisture after vegetation restoration. In contrast, the driving factors for soil respiration estimated for biocrust layers changed from precipitation alone to soil temperature and precipitation after vegetation restoration. We reveal that changes in microbial functional structure play important roles in regulating the effect of vegetation restoration and biocrusts on soil respiration. In addition, vegetation restoration also increases the microbial activity in biocrusted soils. This calls for an improved understanding of the effects of biocrusts on soil respiration under vegetation restoration scenarios to advance our ability to evaluate soil carbon releases from dryland ecosystems. Read the free Plain Language Summary for this article on the Journal blog.

QMEC-based Analysis of the Soil Microbial Functional Potentials across Different Tibetan Plateau Glacier Forelands

Soil microorganisms dominate the biogeochemical cycles of elements in glacier forelands, which continue to expand due to the climate warming. We analyzed the soil microbial functional characteristics among three types of glacier forelands on the Tibetan Plateau: Yulong Glacier (Y), a temperate glacier; Tianshan Urumqi Glacier No.1 (T), a sub-continental glacier; and Laohugou Glacier No.12 (L), a continental glacier. Here, soil microbial functional genes were quantified using quantitative microbial element cycling technology (QMEC). We found that, in the three glacier forelands, the abundances of soil microbial functional genes related to hemicellulose degradation and reductive acetyl-CoA pathway were highest compared with other carbon-related functional genes. The main nitrogen cycling genes were involved in ammonification. The functional genes of the phosphorus cycle and sulfur cycle were related to organic phosphate mineralization and sulfur oxidation. Furthermore, the soils of the temperate glacier foreland with better hydrothermal conditions had the most complex microbial functional gene structure and the highest functional potentials, followed by those of the soils of continental glacier foreland with the driest environment. These significant differences in soil microbial functional genes among the three types of glacier forelands verified the impacts of geographic difference on microbial functional characteristics, as well as providing a basis for the study of soil microbial functions and biogeochemical cycles in glacier forelands.

Variations of soil bacterial microbial community and functional structure under different land-uses

To reveal the differences between land-use patterns and the changes in soil properties, the changes in soil bacterial microbial communities and functions driven by land-use patterns were studied by 16SrRNA Gene Fragments and its high-throughput sequencing, relying on the wetland, farmland and forestland soils in the Hongxing National Nature Reserve of Heilongjiang Province. The study area was slightly acidic soil, and the water content, soil organic carbon content, total soil nitrogen and phosphorus contents of wetland soil were higher [...]

In situ differences in nitrogen cycling related to presence of submerged aquatic vegetation in a Gulf of Mexico estuary

AbstractEstuaries provide a suite of ecosystem services to people but are also under heavy stress from human development including excess nutrient loading and alterations in benthic habitat that affect nutrient cycling. Here we examine the interaction of two important and common ecosystem management priorities in estuaries: limiting eutrophication and restoration of submerged aquatic vegetation (SAV). Rates of benthic nitrogen processing can vary by habitat type and there is need for more complete data on the contribution of SAV to overall nitrogen cycling in estuaries, as well as a need to examine nitrogen cycling in situ to better characterize the role of SAV areal coverage in mediating estuarine eutrophication. We compare nitrogen cycling between two common and adjacent habitat types (SAV and adjacent bare sediment [BS]) in an index coastal estuary using an in situ chamber‐based approach to better capture realized habitat differences. We also examined genomic community structure of sediment bacteria and archaea to identify biological indicators of nitrogen exchange. Both mean sediment–water exchange of dissolved N2 and microbial functional community structure differed between SAV and BS. Habitat differences were more consistent with lower variability at locations with low salinity and when sediment organic content was highest, which aligns with findings in other studies. Habitat types differed significantly in microbial composition, including functional groups and genes, like nifH, that may contribute to observed differences in nitrogen cycling. Overall, habitat type appeared most important to nitrogen cycling near the river mouth where sediment nitrogen was higher, and this information has implications for integrated management of habitat restoration/conservation and nutrient loading.

Soil Microbial Diversity and Community Composition in Rice-Fish Co-Culture and Rice Monoculture Farming System.

Simple SummaryThe integration of fish in rice fields can influence the diversity and structural composition of soil microbial communities. Therefore, soil microorganisms between rice–fish co-culture (RF) and rice monoculture (MC) were compared. The key findings revealed that Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes were the most dominant taxa across both paddy fields. The most abundant genus in MC belonged to Anaeromyxobacter, whereas that in RF was Bacillus. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF. Phosphatase, β-glucosidase, cellulase, and urease enzymes were detected in both paddy fields. However, a 2-year conversion from organic rice to rice–fish co-culture may not be long enough to significantly alter alpha diversity indices.Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility.

Permafrost thaw with warming reduces microbial metabolic capacities in subsurface soils.

Microorganisms are major constituents of the total biomass in permafrost regions, whose underlain soils are frozen for at least two consecutive years. To understand potential microbial responses to climate change, here we examined microbial community compositions and functional capacities across four soil depths in an Alaska tundra site. We showed that a 5-year warming treatment increased soil thaw depth by 25.7% (p = .011) within the deep organic layer (15-25cm). Concurrently, warming reduced 37% of bacterial abundance and 64% of fungal abundances in the deep organic layer, while it did not affect microbial abundance in other soil layers (i.e., 0-5, 5-15, and 45-55cm). Warming treatment altered fungal community composition and microbial functional structure (p < .050), but not bacterial community composition. Using a functional gene array, we found that the relative abundances of a variety of carbon (C)-decomposing, iron-reducing, and sulphate-reducing genes in the deep organic layer were decreased, which was not observed by the shotgun sequencing-based metagenomics analysis of those samples. To explain the reduced metabolic capacities, we found that warming treatment elicited higher deterministic environmental filtering, which could be linked to water-saturated time, soil moisture, and soil thaw duration. In contrast, plant factors showed little influence on microbial communities in subsurface soils below 15cm, despite a 25.2% higher (p < .05) aboveground plant biomass by warming treatment. Collectively, we demonstrate that microbial metabolic capacities in subsurface soils are reduced, probably arising from enhanced thaw by warming.

Long-term combined application of chemical fertilizers and organic manure shapes the gut microbial diversity and functional community structures of earthworms

Earthworms are crucial regulators of many soil ecosystem processes; however, the effects of fertilization regimes on earthworm gut microbiota remains poorly understood. Here, we investigated the effects of 10 years of fertilization on the gut microbiota of two different earthworm species, Metaphire californica and Amynthas phaselus, belonging to anecic and endogeic ecological groups, respectively. Five fertilization treatments were designed as follows: non-nitrogen fertilizer (CK), nitrogen fertilizer only (NPK), and the combined application of inorganic fertilizers and three different application rates of pig manure (NPKM1, NPKM2, NPKM3). We observed that, compared with the CK and NPK treatments, the organic manure treatments had strong effects on both earthworm gut microbial communities and the associated metabolic functions. The lower application rate of organic manure significantly increased the gut microbial diversity of both earthworm species, which may have further improved their gut microbial metabolic potential, especially for the metabolism of various carbon resources. With the increasing application of organic fertilizers, the abundance of several bacterial families, such as Comamonadaceae, Oxalobacteraceae, and Cytophagaceae, significantly increased in the gut of M. californica. These families have also been identified as the primary indicator taxa of high organic matter inputs and play a crucial role in regulating microbial community functionalities. However, a similar trend was not observed in the gut of A. phaselus, indicating that A. phaselus might be less sensitive to fertilization regimes because it lives deeper in the soil and has a long digestive tract compared with those of M. californica. Our results demonstrated that long-term organic amendment application significantly shapes earthworm gut microbial communities and results in greater decomposition potential of the earthworm gut. Furthermore, our study found that lower application rates of organic matter may be beneficial for earthworm gut microbial diversity and functional structures.

Stable Soil Microbial Functional Structure Responding to Biodiversity Loss Based on Metagenomic Evidences.

Anthropogenic disturbances and global climate change are causing large-scale biodiversity loss and threatening ecosystem functions. However, due to the lack of knowledge on microbial species loss, our understanding on how functional profiles of soil microbes respond to diversity decline is still limited. Here, we evaluated the biotic homogenization of global soil metagenomic data to examine whether microbial functional structure is resilient to significant diversity reduction. Our results showed that although biodiversity loss caused a decrease in taxonomic species by 72%, the changes in the relative abundance of diverse functional categories were limited. The stability of functional structures associated with microbial species richness decline in terrestrial systems suggests a decoupling of taxonomy and function. The changes in functional profile with biodiversity loss were function-specific, with broad-scale metabolism functions decreasing and typical nutrient-cycling functions increasing. Our results imply high levels of microbial physiological versatility in the face of significant biodiversity decline, which, however, does not necessarily mean that a loss in total functional abundance, such as microbial activity, can be overlooked in the background of unprecedented species extinction.

Microbial functions and soil nitrogen mineralisation processes in the soil of a cool temperate forest in northern Japan

There is little knowledge about microbial functional community structures and the relationships between microbial communities and nitrogen transformation processes. Here, we investigated the relationships between soil microbial communities and nitrogen mineralisation potentials in a cool temperate forest throughout the growing season. Microbial communities were assessed by quantification of the total bacterial, archaeal, and fungal gene abundances and the bacterial and archaeal amoA gene abundances, functional predictions of bacteria and fungi, and analysis of the bacterial-fungal co-occurrence network. In mid-summer, ectomycorrhizal fungal abundance was significantly higher, whereas the total bacterial abundance was significantly lower. Bacterial and archaeal amoA gene abundances were also significantly higher in mid-summer. However, regardless of the seasonal fluctuation of microbial gene abundances, the net nitrification and nitrogen mineralisation potential did not show clear seasonality. In the network analysis, the microbial community was divided into 13 modules, which were subgroups assumed to have similar niches. Furthermore, two modules that mainly consisted of microbial species of Proteobacteria and Bacteroidetes were significantly and positively correlated with the net nitrification and mineralisation potentials. Our results indicated that microbial subgroups sharing similar niches, instead of total microbial abundances and functional gene abundances, could be important factors affecting the net nitrogen mineralisation potential.

Linking microbial community composition to farming pattern in selenium-enriched region: Potential role of microorganisms on Se geochemistry

Selenium (Se) is an essential micronutrient for lives. Indigenous microbial communities play an important role on Se geochemistry in soils. In this study, the microbial community composition and functions of 53 soil samples were investigated using high-throughput sequencing. Samples were divided into 3 groups with different farming types based on the measured geochemical parameters and microbial functional structures. Results indicated that putative Se related bacteria Bacillus, Dyella, Paenibacillus, Burkholderia and Brevibacillus were dominant in dryland plantation soils which were characterized with higher available Se and low contents of H2O, total organic carbon (TOC), NH4+ and NO2−. In contrast, the putative denitrifier Pseudomonas dominated in flooded paddy soils with higher TOC, NO3− and organic Se, whereas genera Rhizobium, Nitrosospira, and Geobacter preferred woodland soils with higher oxidation-reduction potential (ORP), pH, NH4+ and Fe. Farming patterns resulted in distinct geochemical parameters including moisture, pH, ORP, TOC, and contents of soluble Fe, NO2− and NH4+, shaping the microbial communities, which in turn affected Se forms in soils. This study provides a valuable insight into understanding of Se biogeochemistry in soils and prospective strategy for Se-rich agriculture production.

Stimulation of soil microbial functioning by elevated CO2 may surpass effects mediated by irrigation in a semiarid grassland

The functioning of microbial communities in response to elevated atmospheric carbon dioxide (eCO2) is one of the most important, but poorly understood, contributors to climate change feedbacks. The effect of soil moisture caused by eCO2 on soil microbial communities and functioning may be of high importance in water limited ecosystems. To address this knowledge gap, we measured the functional composition, structure, and functional processes of soil microbial communities under eCO2 and an irrigation treatment simulating water availability with eCO2 at two soil depths (0–5 cm and 5–15 cm) in a mixed-grass semiarid prairie. The overall functional diversity increased and the microbial composition and structure were significantly (P < 0.01) altered in response to eCO2 and irrigation treatments. A greater number of key functional genes involved in soil, i.e. carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling were stimulated under eCO2 than under irrigation treatment. Structural equation modeling (SEM) suggested that eCO2 significantly impacted soil microbial community structure by mediating both soil moisture and plant biomass, while irrigation influenced soil microbial community structure merely via regulation of soil moisture. Moreover, in this water-limited system, soil moisture mediated eCO2 effects on soil microbial functional structure were relatively more important than those mediated by plant activity. The present study further improves our understanding of how global climate change regulates soil microbial functional processes in a semiarid grassland ecosystem.

Warming exacerbates the impact of nutrient enrichment on microbial functional potentials important to the nutrient cycling in shallow lake mesocosms

AbstractShallow lakes, the most numerous waterbodies on Earth, are susceptible to climate warming and nutrient enrichment whose effects on the microbial functional potentials are not yet fully understood, however. Here, we applied a microarray‐based technology termed GeoChip 5.0 to investigate microbial functional genes at the beginning of April in shallow lake ecosystems simulated in mesocosms that have been undergoing nutrient enrichment and warming for 9 yr. Our results showed that warming exacerbated the impact of nutrient enrichment on microbial metabolic potentials and significantly elevated the microbial autotrophy potentials, carbon degradation potentials (e.g., starch, hemicellulose, cellulose, and chitin), and polyphosphate mobilization potentials. We also observed that warming enhanced the impacts of nutrient enrichment on microbial functional gene structure. The combination of warming and nutrient enrichment increased the deterministic effect from phytoplankton, causing higher interlinking of microbial functional genes involved in the carbon, nitrogen, phosphorus, and sulfur cycling in correlation‐based networks. Overall, we propose that the joint effect of warming and nutrient enrichment promoted the autotrophic carbon supply and the heterotrophic carbon demand and changed the carbon fluxes in the experimental mesocosms.

Responses of cyanobacterial aggregate microbial communities to algal blooms

Freshwater lakes are threatened by harmful cyanobacterial blooms, whose basic unit is Cyanobacterial Aggregate (CA). CA-attached bacteria play a significant role through different blooming stages with substantial variation of their taxonomic structure. However, little is known about their functional variations and functional links with cyanobacteria due to the lack of reference genomes. In this longitudinal study, we collected 16 CA samples from Lake Taihu, one of China's largest freshwater lakes, from April 2015 to February 2016, and sequenced their V4 region of 16S rRNA genes, full metagenomes (MG), and metatranscriptomes (MT). The analysis of these data revealed the dynamics of microbial taxonomic and functional structure in CAs, influenced by both external environmental factors and internal metabolism. 55 OTUs, 456 genes, and 37 transcripts showed significantly differential abundance across the early, middle, and late blooming stages (ANOVA test, P < 0.05). Total nitrogen and total phosphorus were proved to be the most important environmental drivers of microbial taxonomic and functional variations in CAs (Mantel's r > 0.25, P < 0.05). We constructed 161 high-quality metagenome-assembled genomes (MAGs), out of which 22 were cyanobacterial strains with diverse energy pathways, transporters and prokaryotic defense systems. Based on these MAGs, we constructed a cyanobacteria-bacteria co-nitrogen-pathway and a cyanobacteria-bacteria co-phosphorus-pathway, by which we demonstrated how nitrogen and phosphorus influence the dynamics of the microbial structure to a certain extent by affecting these co-pathways. Overall, these results characterized the taxonomic, functional, and transcriptional variations of microbes in CAs through different blooming stages. Genome assembly and metabolic analysis of cyanobacteria and their attached bacteria suggested that the material exchange and signal transduction do, indeed, exist among them. Our understanding of the underlying molecular pathways for cyanobacterial blooms could lead to the control of blooms by interventional strategies to disrupt critical microbes' expression.

Edaphic variables are better indicators of soil microbial functional structure than plant-related ones in subtropical broad-leaved forests

Soil microorganisms play important roles in the ecosystem functioning of subtropical broad-leaved forests (SBFs). However, the patterns and environmental indicators of soil microbial functional structure remain unclear in SBFs. In the present work, we used a functional microarray (GeoChip 4.0) to examine the soil microbial functional structure of three types of SBFs, including a deciduous broad-leaved forest (DBF), a mixed evergreen-deciduous broad-leaved forest (MBF), and an evergreen broad-leaved forest (EBF). We found that microbial functional structure was significantly different among SBFs (P < 0.05). Compared to the DBF and the EBF, the MBF had higher functional α-diversity (P = 0.001, F = 12.55) but lower β-diversity (P < 0.001, F = 61.09), and showed more complex functional gene networks. Besides, the MBF had higher relative abundances of functional genes for carbon (C) decomposition, C fixation, nitrogen (N) cycling, sulfur (S) cycling, and phosphorus (P) cycling (P < 0.05), indicating stronger microbial functional capabilities of nutrient cycling processes. Edaphic variables (i.e., soil pH and soil nutrient content) were revealed as better indicators of soil microbial functional structure than plant-related ones (i.e., vegetation type and plant diversity) in SBFs. For example, functional gene structure of the DBF was significantly related to soil total S (P = 0.041), that of the MBF was significantly related to soil organic C (P = 0.027) and plant available P (P = 0.034), and that of the EBF was significantly related to soil pH (P = 0.006) and total potassium (K) (P = 0.038). Overall, through the analysis of microbial functional gene profiles, this study yields unique insights into the environmental indicators of patterns and mechanisms of soil microbial functional structure in SBFs.

Microscale heterogeneity of the soil nitrogen cycling microbial functional structure and potential metabolism.

Soil aggregates, with complex spatial and nutritional heterogeneity, are clearly important for regulating microbial community ecology and biogeochemistry in soils. However, how the taxonomic composition and functional attributes of N-cycling-microbes within different soil particle-size fractions under a long-term fertilization treatment remains largely unknown. Here, we examined the composition and metabolic potential for urease activity, nitrification, N2 O production and reduction of the microbial communities attached to different sized soil particles (2000-250, 250-53 and <53 μm) using a functional gene microarray (GeoChip) and functional assays. We found that urease activity and nitrification were higher in <53 μm fractions, whereas N2 O production and reduction rates were greater in 2000-250 and 250-53 μm across different fertilizer regimes. The abundance of key N-cycling genes involved in anammox, ammonification, assimilatory and dissimilatory N reduction, denitrification, nitrification and N2 -fixation detected by GeoChip increased as soil aggregate size decreased; and the particular key genes abundance (e.g., ureC, amoA, narG, nirS/K) and their corresponding activity were uncoupled. Aggregate fraction exerted significant impacts on N-cycling microbial taxonomic composition, which was significantly shaped by soil nutrition. Taken together, these findings indicate the important roles of soil aggregates in differentiating N-cycling metabolic potential and taxonomic composition, and provide empirical evidence that nitrogen metabolism potential and community are uncoupled due to aggregate heterogeneity.

Large-scale evidence for microbial response and associated carbon release after permafrost thaw.

Permafrost thaw could trigger the release of greenhouse gases through microbial decomposition of the large quantities of carbon (C) stored within frozen soils. However, accurate evaluation of soil C emissions from thawing permafrost is still a big challenge, partly due to our inadequate understanding about the response of microbial communities and their linkage with soil C release upon permafrost thaw. Based on a large-scale permafrost sampling across 24 sites on the Tibetan Plateau, we employed meta-genomic technologies (GeoChip and Illumina MiSeq sequencing) to explore the impacts of permafrost thaw (permafrost samples were incubated for 11days at 5°C) on microbial taxonomic and functional communities, and then conducted a laboratory incubation to investigate the linkage of microbial taxonomic and functional diversity with soil C release after permafrost thaw. We found that bacterial and fungal α diversity decreased, but functional gene diversity and the normalized relative abundance of C degradation genes increased after permafrost thaw, reflecting the rapid microbial response to permafrost thaw. Moreover, both the microbial taxonomic and functional community structures differed between the thawed permafrost and formerly frozen soils. Furthermore, soil C release rate over five month incubation was associated with microbial functional diversity and C degradation gene abundances. By contrast, neither microbial taxonomic diversity nor community structure exhibited any significant effects on soil C release over the incubation period. These findings demonstrate that permafrost thaw could accelerate C emissions by altering the function potentials of microbial communities rather than taxonomic diversity, highlighting the crucial role of microbial functional genes in mediating the responses of permafrost C cycle to climate warming.

土地利用驱动的土壤性状变化影响微生物群落结构和功能

微生物在调节陆地生态系统地球化学循环过程中具有重要作用。土地利用方式改变显著影响土壤微生物群落结构和功能，但对土地利用驱动的土壤性状变化与微生物群落结构和功能关系的研究相对匮乏。依托长期定位监测试验（始于1984年），通过16S rRNA基因片段和ITS高通量测序，研究了土地利用方式（裸地、农田、草地）驱动的土壤碳氮变化对微生物群落结构和功能的影响。结果表明：对于细菌群落而言，裸地中α-多样性最高、其次是草地、农田中最低，农田和草地中细菌优势菌群变形菌（Proteobacteria）和放线菌门（Actinobacteria）相对丰度较裸地低4.5%、3.9%和5.5%、3.8%；对于真菌群落而言，裸地子囊菌门（Ascomycota）相对丰度最高、农田次之、草地最低；化能异养型、好氧化能异养型细菌相对丰度裸地显著高于农田和草地（P<0.05），而硝化型和好氧氨氧化型细菌裸地显著低于农田和草地（P<0.05）；腐生型真菌相对丰度大小排序为：裸地>农田>草地。细菌群落变化主要与土壤容重、全氮、矿质氮、C ： N比和微生物量碳有关，而真菌群落与土壤矿质氮有关。细菌和真菌功能菌群主要受土壤容重、土壤有机碳、土壤全氮、C ： N比和微生物量碳影响。因此，土壤容重、土壤全氮、土壤有机碳、C ： N比、微生物量碳、矿质氮差异可能是影响不同土地利用方式中微生物群落和功能变化的主要因素。;Microorganisms play an important role in regulating biogeochemical cycling in terrestrial ecosystems. Microbial functional structure and related processes are determined by the microbial community. Soil physiochemistry properties affect microbial community structure. Land uses affect soil properties and microbial communities, whereas most of the researches at home and abroad focus on the effect of different land uses on soil properties, and how effect of soil properties variations on microbial community and functional structure under land uses were unclear. In this study, land uses (i.e., bare-land, farmland, and grassland) were selected from the long-field experiment (established in 1984). The experimental plot is located at the Changwu National Field Scientific Observation and Research Station of Farmland Ecosystem in the highland and gully region of Shaanxi Province, which is a dry-farming and rain-fed agricultural area. Soil microbial community structure (16S rRNA and ITS), soil physiochemistry properties have been determined, such as soil bulk density (BD), soil organic carbon (SOC), soil total nitrogen (TN), soil microbial biomass carbon (SMBC), and soil mineral nitrogen (mineral N). We found that there was a significant difference in the relative abundance of microbial communities and functional structure under different land uses. Alpha diversity of soil bacterial community was the highest in bare-land, and followed by grassland and farmland. The relative abundance of Proteobacteria, Actinobacteria, and Ascomycota in the farmland (29.7%, 17.3%, 9.2%) and grassland (29.9%, 17.6%, 5.5%) were lower than in bare-land (31.1%, 18.3%, 27.0%). The relative abundance of chemoheterotrophy and aerobic chemoheterotrophy in the bare-land were significantly higher than those in the farmland and grassland, where nitrification and aerobic ammonia oxidation were significantly lower than those in the farmland and grassland (P<0.05). Saprotrophic fungi were the highest in bare-land, followed by farmland and grassland. Variation of bacterial community structure was influenced by BD, TN, mineral N, C:N ratio, and soil microbial biomass carbon (SMBC), while variation of fungal community structure was mainly influenced by mineral nitrogen. In addition, the functional community structure of both bacteria and fungi were mainly affected by BD, SOC, TN, C:N ratio, and SMBC. Specifically, Proteobacteria, Actinomycetes, Ascomycetes, and Basidiomycetes were more suitable to live in the farmland soil than in grassland. Chemical heterotrophic, aerobic chemical heterotrophic bacteria, and saprophytic fungi, which participated in soil carbon cycle, were mainly enriched in the farmland. Nitrification and aerobic ammonia oxidizing bacteria involved in the nitrogen cycle were mainly concentrated in the grassland. Therefore, the change of soil physiochemistry properties driven by land uses affected the community structure and function of microorganisms. In conclusion, variations of BD, TN, SOC, C:N ratio, SMBC, and mineral N under land uses change dominated the microbial community and functional structure.