Communities In Agricultural Soils Research Articles

The Effect of Clarithromycin Toxicity on the Growth of Bacterial Communities in Agricultural Soils

The presence of antibiotics in different environmental matrices is a growing concern. The introduction of antibiotics into the soil is mainly due to sewage treatment plants. Once in the soil, antibiotics may become toxic to microbial communities and, as a consequence, can pose a risk to the environment and human health. This study evaluates the potential toxicity of the antibiotic clarithromycin (CLA) in relation to the bacterial community of 12 soils with different characteristics. Bacterial community growth was evaluated in soils spiked in the laboratory with different concentrations of CLA after 1, 8, and 42 incubation days. The results indicated that the addition of clarithromycin to the soil may cause toxicity in the bacterial communities of the soil. In addition, it was observed that toxicity decreases between 1 and 8 incubation days, while the bacterial community recovers completely in most soils after 42 incubation days. The results also show that soil pH and effective cation exchange capacity may influence CLA toxicity.

Long-term agricultural management impacts arbuscular mycorrhizal fungi more than short-term experimental drought

Agricultural management practices and extreme weather events associated with climate change can influence the diversity and abundance of arbuscular mycorrhizal fungi (AMF) with potential consequences for crop production. However, the importance of the interactive effects of long-term agricultural management and extreme weather events on AMF communities in agricultural soils is not yet fully explored. A short-term drought experiment with rainout-shelters was performed in winter wheat fields in a long-term agricultural trial with organic (biodynamic) and conventional management practices. During four months of the winter wheat growing period (March–June 2017), the rainout-shelters reduced the ambient precipitation by 65% on average. At two sampling dates, the AMF diversity and community composition were assessed using a single-molecule real-time (SMRT) DNA sequencing. A total of 955 amplicon sequence variants (ASVs), belonging to twelve genera were identified. The long-term farming systems and the short-term experimental drought did not affect AMF ASV diversity levels. The AMF community composition at the genus level differed between the organic and the conventional farming systems, but no distinctive communities were found in response to the experimental drought. The three most abundant genera Acaulospora, Paraglomus and Funneliformis were correlated to the two farming practices. Our study demonstrates that AMF communities in agricultural soils are responsive to long-term farming systems, and are resistant to one short-term summer drought event.

Stochastic community assembly decreases soil fungal richness in arid ecosystems.

Uncovering the linkages between community assembly and species diversity is a fundamental issue in microbial ecology. In this study, a large-scale (transect intervals of 1257.6km) cross-biome soil survey was conducted, which ranged over agricultural fields, forests, wetlands, grasslands and desert, in the arid regions of northwest China. The aim was to investigate the biogeographic distribution, community assembly and species co-occurrence of soil fungi. The fungal communities in agricultural soils exhibited a steeper distance-decay slope and wider niche breadths, and were more strongly affected by stochastic assembly processes, than fungi in other natural habitats. A strong relationship was revealed between soil fungal richness and community assembly in arid ecosystems, with the influence of stochastic assembly processes decreasing with increasing fungal richness. Moreover, aridity was the most important environmental factor influencing fungal richness, β-diversity and species co-occurrence patterns. Specifically, the predicted increase in arid conditions will probably reduce fungal richness and network complexity. These findings represent a considerable advance in linking fungal richness to mechanisms underlying the biogeographic patterns and assembly processes of fungal communities in arid ecosystems. These results can thus be used to forecast species co-occurrence and diversities pattern of soil fungi under climate aridity and land-use change scenarios.

Dissipation of antibiotic resistance genes in manure-amended agricultural soil

Soil antibiotic resistance due to animal manure application is of great concern in recent years. Little is known about the fate of antibiotic resistance genes (ARGs) in agricultural soils associated with long-term manure application. Here we used soil microcosms to investigate the dissipation of ARGs and the change of bacterial community in agricultural soil originated from a vegetable field which had received 24 years' swine manure application. Soil microcosms were conducted at different soil moistures and with or without biochar over a testing period of two years in lab. Results showed that continuous manure application induced an accumulation of ARGs in soil, wherein the dissipation of ARGs differed from those in non-manure amended soil. ARGs persisted in soils at least two years, although their abundance declined gradually. Meanwhile, soil moisture and biochar had significant impact on the fate of ARGs. ARGs dissipated faster in soil with higher moisture. Biochar amendment contributed to the maintenance of bacterial diversity. Within the two years of simulation experiment, biochar enhanced soil ARG retention as they dissipated slowly in the soil amended with biochar. Succession of microbial community may have sustained the transfer and resilience of ARGs. This study provides insight into the dissipation of antibiotic resistance genes in manure-applied agricultural soil.

Biochar decreased enantioselective uptake of chiral pesticide metalaxyl by lettuce and shifted bacterial community in agricultural soil

A 35-day microcosmic experiment was conducted with lettuce (Lactuca sativa L.) and two metalaxyl (MET) enantiomers (R-MET and S-MET) to understand the roles of biochar in the enantioselective fate of chiral pesticides in soil-plant ecosystems. Wood waste-derived biochar (WBC) amendment effectively decreased the shoot concentrations of R-MET/S-MET and their metabolites R-MET/S-MET acid by 57.7–86.3% and 13.3–32.5%, respectively. The reduced uptake was mainly attributed to the decreased bioavailability of R-MET and S-MET. A lower fraction of R-MET was accumulated by the lettuce in the WBC-amended soils relative to the control, suggesting a decrease in the enantioselective uptake of the chiral pesticide MET in the presence of biochar. Regardless of the WBC amendment, no enantiomerization of MET or MET acid occurred. The application of WBC stimulated soil bacterial diversity, shifted the bacterial community, and enhanced the abundance of pesticide degrading bacteria (e.g., Luteimonas, Methylophilus, and Hydrogenophaga), which were responsible for the enantioselective degradation of MET in the soil. This work expands our understanding of the enantioselective fate of chiral pesticides in the biochar-amended soil ecosystems. These findings can be used to develop biochar-based technologies to remediate soils contaminated with these chiral pesticides to ensure food safety.

Community assembly mechanisms and co-occurrence patterns of nitrite-oxidizing bacteria communities in saline soils

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification by oxidizing nitrite to nitrate, which is a key process in the biogeochemical nitrogen cycling. However, little is known about the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. Here, we explored the effects of salinity on Nitrobacter and Nitrospira community using high-throughput sequencing and multivariate statistical analyses. Our results showed that high salinity significantly inhibited the nitrite oxidation rates and decreased the abundance of Nitrobacter and Nitrospira. Extreme salty conditions significantly altered the diversity and composition of Nitrospira community but had little effect on Nitrobacter community. Nitrobacter network in high salinity soils was more closely connected while the connectivity of Nitrospira network became weak. Nitrobacter and Nitrospira community exhibited distinct assembly processes at different salinity levels. Stochastic processes were dominant in the Nitrobacter community assembly in both low and high salinity soils. Interestingly, the assembly of Nitrospira community was governed by stochastic and deterministic processes in low and high salinity soils, respectively. To our knowledge, our study provides the first description of the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. These results can help us understand the NOB ecological roles and improve the nitrite oxidation activity in a high salinity environment.

The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa, USA.

This study investigated the differences in microbial community abundance, composition and diversity throughout the depth profiles in soils collected from corn and soybean fields in lowa, USA using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities at increasing soil depth. Soil microbial community composition differed due to crop type only in the top 60 cm and due to location only in the top 90 cm. While the relative abundance of most phyla decreased in deep soils, the relative abundance of the phylum Proteobacteria increased and dominated agricultural soils below the depth of 90 cm. Although soil depth was the most important factor shaping microbial communities, edaphic factors including soil organic matter, soil bulk density and the length of time that deep soils were saturated with water were all significant factors explaining the variation in soil microbial community composition. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. A greater understanding of how soil depth influences the diversity and composition of soil microbial communities is vital for guiding sampling approaches in agricultural soils where plant roots extend beyond the upper soil profile. In the long term a greater knowledge of the influence of depth on microbial communities should contribute to new strategies that enhance the sustainability of soil which is a precious resource for food security.IMPORTANCE Determining how microbial properties change across different soils and within the soil depth profile, will be potentially beneficial to understanding the long-term processes that are involved in the health of agricultural ecosystems. Most literature on soil microbes has been restricted to the easily accessible surface soils. However, deep soils are important in soil formation, carbon sequestration, and in providing nutrients and water for plants. In the most productive agricultural systems in the USA where soybean and corn are grown, crop plant roots extend into the deeper regions of soils (> 100 cm), but little is known about the taxonomic diversity or the factors that shape deep soil microbial communities. The findings reported here highlight the importance of soil depth in shaping microbial communities, provide new information about edaphic factors that influence the deep soil communities and reveal more detailed information on taxa that exist in deep agricultural soils.

Multifunctionality and microbial communities in agricultural soils regulate the dynamics of a soil-borne pathogen

Determining the soil factors that drive the dynamics of soil-borne pathogens is an essential step toward the formulation and implementation of strategies for the control of plant diseases. We sampled 48 healthy and infected soils in peanut fields from six counties in Eastern China to explore the relationships between soil multifunctionality, microbial communities, and peanut stem rot pathogen, Athelia rolfsii. The results showed that peanut stem rot infection did not affect soil microbial richness, but it increased soil multifunctionality, altered the microbial community composition, and decreased the complexity of microbial co-occurrence networks significantly. Soil biotic and abiotic factors had markedly effects on A. rolfsii, and specific soil functions and microbial taxa were significantly associated with A. rolfsii abundance. Soil multifunctionality and microbial community compositions negatively affected A. rolfsii abundance, while the effects of bacterial and fungal richness were contrasting for healthy and infected soils. Longitude and latitude indirectly and positively affected A. rolfsii abundance. The results demonstrate that soil multifunctionality and microbial communities play a vital role in regulating the dynamics of peanut stem rot pathogen, which could enhance our understanding of the relationships between soil factors, pathogen dynamics, and plant health.

Bioremediation by Cupriavidus metallidurans Strain MSR33 of Mercury-Polluted Agricultural Soil in a Rotary Drum Bioreactor and Its Effects on Nitrogen Cycle Microorganisms.

Nitrogen cycle microorganisms are essential in agricultural soils and may be affected by mercury pollution. The aims of this study are to evaluate the bioremediation of mercury-polluted agricultural soil using Cupriavidus metallidurans MSR33 in a rotary drum bioreactor (RDB) and to characterize the effects of mercury pollution and bioremediation on nitrogen cycle microorganisms. An agricultural soil was contaminated with mercury (II) (20–30 ppm) and subjected to bioremediation using strain MSR33 in a custom-made RDB. The effects of mercury and bioremediation on nitrogen cycle microorganisms were studied by qPCR. Bioremediation in the RDB removed 82% mercury. MSR33 cell concentrations, thioglycolate, and mercury concentrations influence mercury removal. Mercury pollution strongly decreased nitrogen-fixing and nitrifying bacterial communities in agricultural soils. Notably, after soil bioremediation process nitrogen-fixing and nitrifying bacteria significantly increased. Diverse mercury-tolerant strains were isolated from the bioremediated soil. The isolates Glutamicibacter sp. SB1a, Brevundimonas sp. SB3b, and Ochrobactrum sp. SB4b possessed the merG gene associated with the plasmid pTP6, suggesting the horizontal transfer of this plasmid to native gram-positive and gram-negative bacteria. Bioremediation by strain MSR33 in an RDB is an attractive and innovative technology for the clean-up of mercury-polluted agricultural soils and the recovery of nitrogen cycle microbial communities.

Depression of Groundwater Table and Reduced Nitrogen Application Jointly Regulate the Bacterial Composition of nirS-Type and nirK-Type Genes in Agricultural Soil

Despite the known influence of nitrogen fertilization and groundwater conditions on soil microbial communities, the effects of their interactions on bacterial composition of denitrifier communities have been rarely quantified. Therefore, a large lysimeter experiment was conducted to examine how and to what extent groundwater table changes and reduced nitrogen application would influence the bacterial composition of nirK-type and nirS-type genes. The bacterial composition of nirK-type and nirS-type genes were compared at two levels of N input and three groundwater table levels. Our results demonstrated that depression of groundwater table, reduced nitrogen application and their interactions would lead to drastic shifts in the bacterial composition of nirS-type and nirK-type genes. Structural equation models (SEMs) indicated that depression of groundwater table and reduced nitrogen application not only directly altered the species composition of denitrifier bacterial communities, but also indirectly influenced them through regulating soil nutrient and salinity. Furthermore, the variation in soil NO3−–N and electrical conductivity caused by depression of groundwater table and reduced nitrogen application played the most important role in altering the community composition of denitrifier bacterial communities. Together, our findings provide first-hand evidence that depression of groundwater table and reduced nitrogen application jointly regulate the species composition of denitrifier bacterial communities in agricultural soil. We highlight that local environmental conditions such as groundwater table and soil attributes should be taken into account to enrich our knowledge of the impact of nitrogen fertilization on soil denitrifier bacterial communities, or even biogeochemical cycles.

Quantitative estimation of stochastic and deterministic processes for soil prokaryotic community assembly in the Yellow River floodplain

AbstractThe floodplain ecosystem plays an important role in the mediation or regulation of regional ecological functions, and is the heart of ecosystem functions based on soil microbial communities. In the present study, we investigate the patterns and assembly processes of soil microbial communities along nine profile depths (up to 280 cm in depth) of three stages of floodplain community succession (channel bar, newly deposited river beach and tender floodplain) and farmland in the floodplain of the lower Yellow River. Generally, the bacterial community in agricultural soil had the highest diversity, whereas the archaeal community in the tender floodplain had the highest diversity. Compared to bacteria, the co‐occurrence network of archaea was more complex and stable and had high connectivity. Our data suggest that the resistance of bacteria and archaea to environmental changes in deep soil was higher when compared to that in surface soil. Furthermore, stochastic and deterministic processes acted concurrently to regulate the assembly of the soil microbial community in the floodplain ecosystems. However, the relative contributions of the stochastic process and deterministic process are different between the bacterial community and the archaeal community. The lowest contribution of the stochastic process in the bacterial community was in the subsoil, whereas in the archaeal community, it was the opposite. For ecological selection, bacterial communities in different soil profiles, in the succession stages and in the farmland, were mainly selected through homogeneous selection, whereas archaeal communities were selected through heterogeneous selection. Compared with the three floodplain succession stages, the microbial communities of agricultural lands were more assembled by deterministic processes.Highlights Stochastic and deterministic processes act concurrently to regulate the assembly of soil microbial community in the floodplain ecosystems. The assembly of the bacterial community was mainly affected by the homogeneous selection. The archaeal community was mainly affected by the heterogeneous selection. The microbial communities of agricultural lands were more assembled by deterministic processes.

Ecological impact of organochlorine pesticides consortium on autochthonous microbial community in agricultural soil

Organochlorine pesticides (OCPs) used in agricultural practices are of global concern due to their toxicological hazards on biomes of the impacted soil. Geochemistry and microbiome of OCPs-impacted (OW) soil was determined and compared with those of pristine (L1) soils. Microbiome of OW was based on sequencing total 16S rRNA genes of prokaryotes and Internal Transcribed Spacer (ITS2) regions between 5.8S and 28S rRNA genes of eukaryotes using Illumina MiSeq platform for bacterial and fungal communities, respectively. Geochemical properties of OW were assessed for ecological risks of OCPs on biota via risk quotient (RQ) and maximum cumulative ratio (MCR). It was established OW was polluted with 15 OCPs, along with consequential nitrate and phosphorous deficiencies. Ten of the 15 OCPs exerted severe ecological risk (RQ > 1: 4–992), of which endosulfan contributed 76% of the ecotoxicity (MCR = 1.3) on OW. The key players in OW were observed to be Enterobacteriaceae and Mortierellaceae represented by Escherichia and Mortierella taxa, respectively. Low abundance of Nitrospirae species and extinction of Glomeromycota in OW connoted serious toxicological consequences of the OCPs. Taxon XOR (Taxon Exclusive Or) analysis revealed 38,212 and 63,474 counts of bacterial and fungal species, respectively, were exclusively found in the impacted OW and possibly contributed to natural attenuation of the OCPs in the impacted agricultural soil. Conversely, 61,005 (bacteria) and 33,397 (fungi) species counts that were missing in OCPs-impacted OW, but present in pristine L1, opined the species as bio-indicators of OCPs ecotoxicity in agricultural soils. While the species tagged as bio-indicators would be valuable in monitoring OCPs pollution, those suggested to be players in self-recovery process will be invaluable to designing bioremediation strategies for OCPs-impacted agricultural soil.

Unraveling the Complexity of Soil Microbiomes in a Large-Scale Study Subjected to Different Agricultural Management in Styria.

Healthy soil microbiomes are crucial for achieving high productivity in combination with crop quality, but our understanding of microbial diversity is still limited. In a large-scale study including 116 composite samples from vineyards, orchards and other crops from all over Styria (south-east Austria), agricultural management as well as distinct soil parameters were identified as drivers of the indigenous microbial communities in agricultural soils. The analysis of the soil microbiota based on microbial profiling of prokaryotic 16S rRNA gene fragments and fungal ITS regions revealed high bacterial and fungal diversity within Styrian agricultural soils; 206,596 prokaryotic and 53,710 fungal OTUs. Vineyards revealed a significantly higher diversity and distinct composition of soil fungi over orchards and other agricultural soils, whereas the prokaryotic diversity was unaffected. Soil pH was identified as one of the most important edaphic modulators of microbial community structure in both, vineyard and orchard soils. In general, the acid-base balance, disorders in the soil sorption complex, content and quality of organic substance as well as individual nutrients were identified as important drivers of the microbial community structure of Styrian vineyard and orchard soils. However, responses to distinct parameters differed in orchards and vineyards, and prokaryotic and fungal community responded differently to the same abiotic factor. In comparison to orchards, the microbiome of vineyard soils maintained a higher stability when herbicides were applied. Orchard soils exhibited drastic shifts within community composition; herbicides seem to have a substantial impact on the bacterial order Chthoniobacterales as well as potential plant growth promoters and antagonists of phytopathogens (Flavobacterium, Monographella), with a decreased abundance in herbicide-treated soils. Moreover, soils of herbicide-treated orchards revealed a significantly higher presence of potential apple pathogenic fungi (Nectria, Thelonectria). These findings provide the basis to adapt soil management practices in the future in order to maintain a healthy microbiome in agricultural soils.

Image-based quantification of soil microbial dead zones induced by nitrogen fertilization

Microbial communities in agricultural soils underpin many ecosystem services including the maintenance of soil structure, food production, water purification and carbon storage. However, the impact of fertilization on the health of microbial communities is not well understood. This study investigates the spatial and temporal dynamics of nitrogen (N) transport away from a fertilizer granule with pore scale resolution. Specifically, we examined how soil structure and moisture content influence fertilizer derived N movement through the soil pore network and the subsequent impact of on soil microbial communities. We develop a mathematical model to describe N transport and reactions in soil at the pore-scale. Using X-ray Computed Tomography scans, we reconstructed a microscale description of a soil-pore geometry as a computational mesh. Solving two-phase water/air model produced pore-scale water distributions at 15, 30 and 70% water-filled pore volume. The N-speciation model considered ammonium (NH4+), nitrate (NO3−) and dissolved organic N (DON), and included N immobilization, ammonification and nitrification processes, as well as diffusion in soil solution. We simulated the dissolution of a fertilizer pellet and a pore scale N cycle at three different water saturations. To aid interpretation of the model results, microbial activity at a range of N concentrations was measured. The model showed that the diffusion and concentration of N in water films is critically dependent upon soil moisture and N species. We predict that the maximum NH4+ and NO3− concentrations in soil solution around the pellet under dry conditions are in the order of 1 × 103 and 1 × 104 mol m−3 respectively, and under wet conditions 2 × 102 and 1 × 103 mol m−3, respectively. Supporting experimental evidence suggests that these concentrations would be sufficient to reduce microbial activity in the short-term in the zone immediately around the fertilizer pellet (ranging from 0.9 to 3.8 mm), causing a major loss of soil biological functioning. This model demonstrates the importance of pore-scale processes in regulating N movement and their interactions with the soil microbiome.

Effects of straw and its biochar applications on the abundance and community structure of CO2-fixing bacteria in a sandy agricultural soil

Crop straw and biochar application can potentially increase carbon sequestration and lead to changes in the microbial community in agricultural soils. Sequestration of CO2 by autotrophic microorganisms is key to biogeochemical carbon cycling in soil ecosystems. The effects of straw and its biochar, derived from slow pyrolysis, on CO2 fixation bacteria in sandy soils, remain unclear. Therefore, this study compared the response of abundance and community of CO2 fixation bacteria to the two straw application methods in a sandy agricultural soil. The overall aim of the study was to achieve an efficient use of straw residues for the soil sustainablility. We investigated the soil organic carbon content and autotrophic bacteria over four consecutive years (2014–2018) in a field experiment, including the following four treatments: whole maize straw amendment (S), whole maize straw translated biochar amendment (B), half biochar and half straw amendment (BS), and control (CK) without straw or biochar amendment. The autotrophic bacterial abundance and community structure were measured using molecular methods of real-time PCR, terminal restriction fragment length polymorphisms (T-RFLP), and a clone library targeting the large subunit gene (cbbL) of ribulose-1,5-bisphosphate carboxylase/oxygenase. The results showed that the content of soil total organic carbon (TOC), dissolved organic carbon (DOC), and microbial biomass carbon (MBC) in B, S, and BS treatments was significantly increased compared with the CK treatment. Soil TOC and available potassium (AK) in the B treatment significantly increased by 15.4% and 23.3%, respectively, but soil bulk density, DOC, and MBC significantly decreased by 8.5%, 10.6%, and 14.5%, respectively, compared with the S treatment. The abundance of the cbbL gene as well as of the bacterial 16S rRNA gene increased significantly in straw or biochar application treatments as compared to the CK treatment. The B treatment, but not the BS treatment, significantly increased the cbbL gene abundance when compared to the S treatment. No significant differences were observed in the bacterial 16S rRNA gene abundance among the three straw or biochar applications. The application of straw biochar could increase the diversity of the autotrophic bacteria, which also altered the overall microbial composition. Physicochemical properties of the soil, such as soil pH, SOC, and bulk density, can help explain the shift in soil microbial composition observed in the study. Taken together, our results suggest that straw biochar, rather than straw application, leads to an increase in the abundance and diversity of CO2-fixing bacteria, which would be advantageous for soil autotrophic CO2 fixation.

Effect of Maize Straw Biochar on Bacterial Communities in Agricultural Soil.

Biochar has become a popular soil amendment. However, its effect on soil microbial community is still unclear. In the present study, maize straw biochar was pyrolysed at 300°C, 450°C and 600°C, respectively, and then was added to agricultural soil at the ratio of 0.5%, 1% and 2%. Bacterial dynamics was analyzed in the pot experiments using denaturing gradient gel electrophoresis. The results indicated that the pyrolysis temperature has great impact on the elemental composition, pH and porous structures of biochar. Moreover, pyrolysis temperature was primary factor to drive the variation of bacterial community structure in biochar amended soil. In addition, the results suggested that biochar amendments on agricultural soil would decrease the bacterial diversity, and selectively promote growth of functional bacteria to become the dominant community, which could increase the bacterial community organization and improve the stability of bacteria to counteract effects of perturbation.

Evidence for niche differentiation of nitrifying communities in grassland soils after 44 years of different field fertilization scenarios

Long-term nitrogen (N) fertilization imposes strong selection on nitrifying communities in agricultural soil, but how a progressively changing niche affects potentially active nitrifiers in the field remains poorly understood. Using a 44-year grassland fertilization experiment, we investigated community shifts of active nitrifiers by DNA-based stable isotope probing (SIP) of field soils that received no fertilization (CK), high levels of organic cattle manure (HC), and chemical N fertilization (CF). Incubation of DNA-SIP microcosms showed significant nitrification activities in CF and HC soils, whereas no activity occurred in CK soils. The 44 years of inorganic N fertilization selected only 13C-ammonia-oxidizing bacteria (AOB), whereas cattle slurry applications created a niche in which both ammonia-oxidizing archaea (AOA) and AOB could be actively 13C-labeled. Phylogenetic analysis indicated that Nitrosospira sp. 62-like AOB dominated inorganically fertilized CF soils, while Nitrosospira sp. 41-like AOB were abundant in organically fertilized HC soils. The 13C-AOA in HC soils were affiliated with the 29i4 lineage. The 13C-nitrite-oxidizing bacteria (NOB) were dominated by both Nitrospira- and Nitrobacter-like communities in CF soils, and the latter was overwhelmingly abundant in HC soils. The 13C-labeled nitrifying communities in SIP microcosms of CF and HC soils were largely similar to those predominant under field conditions. These results provide direct evidence for a strong selection of distinctly active nitrifiers after 44 years of different fertilization regimes in the field. Our findings imply that niche differentiation of nitrifying communities could be assessed as a net result of microbial adaption over 44 years to inorganic and organic N fertilization in the field, where distinct nitrifiers have been shaped by intensified anthropogenic N input.

Biochar-induced migration of tetracycline and the alteration of microbial community in agricultural soils

Recently, biochar is widely used as a soil amendment to improve soil properties, which might affect the fate and behavior of contaminants in soil. In this study, we investigated the effect of biochar on the migration of tetracycline (TC) in soil and their combined impacts on microbiome. Due to the strong interaction between soil and TC, adsorption, rather than photolysis or biodegradation, was the dominating dissipation way of TC in soil. Moreover, biochar could promote the vertical migration of TC through the decreased soil bulk density and its lower adsorption capacity. After 90-day incubation, only slight impact of TC on soil bacterial community was observed due to the rapid dissipation of TC in soil, whereas more available C supply induced by biochar significantly altered bacterial community via the enhancement of copiotrophic bacteria. Besides, biochar could decrease the soil pH and thus change the composition of fungal community. The effect of TC on fungal community was partially counteracted by biochar, which could adsorb part of TC and thus decrease the contact of TC with microorganisms. This work will improve our understanding of the fate of organic pollutants and evolution of microbiome in soil where biochar servers as soil amendment.

Chitin degradation and the temporary response of bacterial chitinolytic communities to chitin amendment in soil under different fertilization regimes

Chitin amendment is a promising agricultural management strategy to control fungal and nematodal plant diseases and to improve crop yield. Chitin degradation in the soil contributes significantly to carbon and nitrogen cycling in terrestrial ecosystems. However, little is known about chitin degradation and bacterial chitinolytic communities in agricultural soil under different fertilization regimes. Thus, in the present study, a 42-day soil incubation experiment was conducted, in which soil under four fertilization regimes (i.e., no fertilization (CK), chemical fertilizer (CF), pig manure plus 50% chemical fertilizer (PMCF), and rice straw plus 100% chemical fertilizer (SRCF)) were amended or not with chitin or its monomer, N-acetylglucosamine (NAG). Different nitrogen forms and CO2 and N2O emission were measured to evaluate chitin degradation and its environmental implications. SRCF soil had the highest CO2 emission, chitin N mineralization, and fungal abundance. NAG and chitin were enriched to exploit the chitin degraders. High-throughput sequencing analyses reveled that Streptomycetaceae, Oxalobacteraceae, Gemmatimonadaceae, and Acidobacteria were generally increased upon chitin amendment in CK, CF, and PMCF soil, whereas Streptomycetaceae dominated chitin-amended SRCF soil. Herpetosiphonaceae was enriched only in chitin-amended CK soil. LEfSe and network analysis were used to predict chitinolytic and opportunistic species, and revealed that most previously reported chitinolytic bacteria were detected in the present study and new potential chitin degraders, including unidentified_Solibacterales, Gemmatimonadaceae, and Herpetosiphonaceae, were identified. Some members of Firmicutes, Actinobacteria, and Proteobacteria, including Bacillus, and Kitasatospora, were speculated to be opportunistic species. The findings improve our understanding of the effects of chitin degradation on carbon and nitrogen cycling in agricultural soil under different fertilization regimes and help to identify chitinolytic bacteria.

Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China

PurposeTo understand which environmental factors influence the distribution and ecological functions of bacteria in agricultural soil.MethodA broad range of farmland soils was sampled from 206 locations in Jilin province, China. We used 16S rRNA gene-based Illumina HiSeq sequencing to estimated soil bacterial community structure and functions.ResultThe dominant taxa in terms of abundance were found to be, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, and Proteobacteria. Bacterial communities were dominantly affected by soil pH, whereas soil organic carbon did not have a significant influence on bacterial communities. Soil pH was significantly positively correlated with bacterial operational taxonomic unit abundance and soil bacterial α-diversity (P<0.05) spatially rather than with soil nutrients. Bacterial functions were estimated using FAPROTAX, and the relative abundance of anaerobic and aerobic chemoheterotrophs, and nitrifying bacteria was 27.66%, 26.14%, and 6.87%, respectively, of the total bacterial community. Generally, the results indicate that soil pH is more important than nutrients in shaping bacterial communities in agricultural soils, including their ecological functions and biogeographic distribution.