Community structure of bacteria on different types of mineral particles in a sandy soil

Various types of mineral particles in a soil probably provide different microenvironments for microorganisms. The purpose of this study is to investigate whether different types of mineral in a soil harbor different bacterial populations. DNA was extracted from five types (quartz, feldspar, pyroxene, magnetite, iron-coated reddish brown particles) of sand-size mineral particles separated from a sandy soil, and was amplified for partial 16 S rRNA gene by polymerase chain reaction (PCR). Twenty-nine to 69 amplicons per each type of mineral were cloned and sequenced, followed by phylogenetic affiliation of the sequences. As a result, some types of bacteria were detected on all of the types of mineral including the orders Rhizobiales, Bacillales, and Acidobacteriales. In the case of Acidobacteriales, higher percentages were found on magnetite and quartz. Some taxa were restricted to specific types of mineral; the class Actinobacteria was found on pyroxene but not on quartz, and rarely on magnetite and feldspar. Bacterial diversity at the order level estimated by Chao1 value was higher in feldspar and pyroxene than the other three types of mineral. The UniFrac Significance test indicated that the differences in bacterial communitiy structures among the particles were suggestive except that between feldspar and pyroxene. These results support the idea that different communities of bacteria were associated with each of the mineral types.     

Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter

Abstract

We studied the effects of the application of organic matter (OM) and chemical fertilizer (CF) on soil alkaline phosphatase (ALP) activity and ALP-harboring bacterial communities in the rhizosphere and bulk soil in an experimental lettuce field in Hokkaido, Japan. The ALP activity was higher in soils with OM than in soils with CF, and activity was higher in the rhizosphere for OM than in the bulk soil. Biomass P and available P in the soil were positively related to the ALP activity of the soil. As a result, the P concentration of lettuce was higher in OM soil than in CF soil. We analyzed the ALP-harboring bacterial communities using polymerase chain reaction based denaturing gradient gel electrophoresis (DGGE) on the ALP genes. Numerous ALP genes were detected in the DGGE profile, regardless of sampling time, fertilizer treatment or sampled soil area, which indicated a large diversity in ALP-harboring bacteria in the soil. Several ALP gene fragments were closely related to the ALP genes of Mesorhizobium loti and Pseudomonas fluorescens. The community structures of the ALP-harboring bacteria were assessed using principal component analysis of the DGGE profiles. Fertilizer treatment and sampled soil area significantly affected the community structures of ALP-harboring bacteria. As the DGGE bands contributing to the principal component were different from sampling time, it is suggested that the major bacteria harboring the ALP gene shifted. Furthermore, there was, in part, a significant correlation between ALP activity and the community structure of the ALP-harboring bacteria. These results raise the possibility that different ALP-harboring bacteria release different amounts and/or activity of ALP, and that the structure of ALP-harboring bacterial communities may play a major role in determining overall soil ALP activity.     

Changes in proteolytic bacteria in paddy soils in response to organic management

Proteolytic bacterial communities, which mineralize organic nitrogen, play a key role in agricultural systems. In this study, alkaline metalloprotease (apr) gene fragments from proteolytic bacteria were investigated in bulk and rhizosphere paddy soil from four fields under organic management (for 2, 3, 5, and 9 years), and from one field under conventional management (for 2 years). We analyzed the abundance and structure of the proteolytic bacterial communities using real-time quantitative PCR and denaturing gradient gel electrophoresis. Our results showed that the abundance of proteolytic bacteria ranged from 1.57?×?10⁸ to 8.02?×?10⁸?copies/g of soil. In addition, the abundance of the proteolytic bacteria in the paddy soils under organic management was significantly higher than those in the paddy soil under conventional management. Moreover, the gene copy numbers in the rhizosphere soils were significantly higher than those in the bulk soils. The abundance of proteolytic bacteria tended to increase with the duration of organic management, with the highest abundance being found in the soil that had been under organic management for 5 years. However, the proteolytic bacteria communities in the paddy soils were not significantly affected by management practices. Phylogeny analysis showed that all gel bands obtained represented genes from Pseudomonas. Additionally, correlation analysis and canonical correspondence analysis showed that C/N, C, and N were important factors that influenced the abundance and community structure of the proteolytic bacteria. These results suggest that proteolytic bacteria are indicators in organic management systems, depolymerize organic N and hence maintain soil sustainability.

Abbreviations: CM: conventional management; OM: organic management; DGGE: denaturing gradient gel electrophoresis; qPCR: real-time quantitative PCR detecting system; COFCC: China organic food certification center; CCA: canonical correspondence analysis     

Analysis of bacterial communities in soil by PCR-DGGE targeting protease genes

We studied the effects of the application of organic (OM) and inorganic fertilizer (CF) on soil protease activity and proteolytic bacterial communities in rhizosphere and bulk soil on an experimental lettuce field in Hokkaido, Japan. The protease activity always was higher in soils of the OM than with the CF treatment, and also higher in the rhizosphere than in the bulk soil. We analyzed proteolytic bacterial communities by denaturing gradient gel electrophoresis (DGGE) of the alkaline metalloprotease (apr) and neutral metalloprotease (npr) genes. Most apr forms detected were closely related to apr of Pseudomonas fluorescens, and all npr variants closely resembled the gene of Bacillus megaterium. These results were consistent with findings from tests using cultured bacterial communities, indicating a high specificity of our PCR-DGGE for amplifying apr and npr genes. The community compositions of proteolytic bacteria were assessed by principal component analysis of the DGGE profiles. There were significant differences in the effects of CF and OM on the community compositions of apr- and npr-expressing bacteria, and the communities of the two types of bacteria played different roles in rhizosphere and bulk soil. We found significant correlations between the protease activity and the communities of the two types of bacteria. The results indicate that different proteolytic bacteria release different amounts or activities of protease, and that the composition of proteolytic bacterial communities may play a major role in determining overall soil protease activity.     

Alphaproteobacteria communities depend more on soil types than land managements

Soil properties and agricultural practices take a joint effect on the communities of soil bacteria. The aim of the present study was to survey Alphaproteobacterial communities as possible indicators of soil quality considering clay, loamy and sandy soils under conventional and organic farming. Alphaproteobacteria community composition were analysed by 16S rRNA gene with nested-PCR (polymerase chain reaction) and denaturing gradient gelelectrophoresis (DGGE). Sequencing of partial 16S rRNA gene from the DGGE bands were performed. Conventional and organic farming resulted in significant differences in chemical properties of soils. According to the results community fingerprints were separated into groups depending on soil types and farming systems. This separation can be attributed mostly to soil pH, AL-P₂O₅,-K₂O. The analysed sequences were identified as soil bacteria which could play the main role in nitrogen fixing, mineralisation and denitrification. The highest diversity index was revealed from the organic farming at sandy texture site, where mainly Mesorhizobium sp. and Rhizobium sp. were detected. The soil type and actual crop could have a stronger impact on the soil bacterial composition than the management.     

Ecological evaluation of polymetallic soil quality: the applicability of culture-dependent methods of bacterial communities studying

Purpose

This work aimed to study the effect of long-term polymetallic contamination on the state and parameters of soil bacterial communities, including the abundance of different groups of culturable bacteria and the activity of nitrification.

Materials and methods

Monitoring plots were located in the dry lake and surrounding area, which had been formerly used for the discharge of industrial waste. The soils in the 16 plots were characterized by extremely high levels of heavy metal pollution. This study evaluated the main soil physicochemical properties by various methods, total metal contents by X-ray analysis, mobile metal content by atomic absorption spectrophotometry, the abundance of chosen groups of culturable bacteria by inoculation on solid media, and nitrification activity from ammonium and nitrite oxidation rates.

Results and discussion

High adaptation capacity of microbial communities to long-term pollution was revealed through marked lack of decrease in the abundance of some of the bacterial groups in soils with high contamination levels. Among the bacteria determined by the colony count method, copiotrophic and spore-forming bacteria were the least sensitive to contamination, and actinomycetes were the most sensitive. The high levels of soil pollution with heavy metals had pronounced adverse effects on nitrification activity. The decrease in activity was strongly correlated with pollutant concentrations. The oxidation of nitrite was shown to be more affected by pollution that the oxidation of ammonium.

Conclusions

Some groups and parameters of culturable microorganisms can be used for soil status estimation under pollution conditions even though they are only a small fraction of the microbial community. The most sensitive parameter was the nitrification rate, while the number of actinomycetes was found to be most promising parameter among the groups of bacteria determined by plate counts. The use of sensitive groups of culturable microorganisms for bioindication purposes is a method, which may provide a cheap and sufficiently reliable tool for large-scale soil monitoring studies.

     

Adsorption of Pseudomonas putida on soil particle size fractions: effects of solution chemistry and organic matter

Purpose  

Attachment of bacteria on soil particles is ubiquitous and governs the transformation of nutrients and degradation of pollutants in soil and associated environments. The nature on the binding of bacteria by soil particles has remained unclear. The objectives of the present study were to investigate the adsorption of Pseudomonas putida on particle size fractions from an Ultisol as influenced by solution chemistry and organic matter.     

沂蒙山林区不同植物群落的土壤颗粒分形与水分入渗特征

为探索沂蒙山林区不同植被对土壤分形结构及入渗性能的改良作用与机制,运用土壤分形学和水文学原理与方法,研究沂蒙山林区7种植物群落下的土壤颗粒组成和入渗过程。结果表明：1）植物群落具有显著改善土壤颗粒结构和入渗性能的作用,其改善程度为针阔叶（赤松＋麻栎）混交林依次高于阔叶林（刺槐纯林、麻栎纯林）和针叶林（赤松纯林）;2）研究区土壤颗粒组成具有石质山地典型粗骨土的结构特征,其分形维数与土壤入渗速率呈明显的正相关关系;3）植物群落改良土壤分形结构和入渗性能的分形学机制,是通过增加土壤粉粒与黏粒等细粒物质含量而提高土壤分形维数,进而改善土壤团粒结构和孔隙结构,提高土壤质地均匀程度和入渗能力的。研究成果可为沂蒙山区水土保持植被类型的合理选择与配置提供参考。     

The drivers of soil bacterial communities in rubber plantation at local and geographic scales

ABSTRACT

According to traditional biogeographic theory, historical contingency can influence soil microbial communities. Thus, we ask: are historical contingencies (soil profiles and geographic sampling locations), or other factors (seasonal changes and soil nutrients), important drivers of soil bacterial communities? This study used high throughput sequencing technology to investigate the soil bacterial compositions of rubber plantations at the local and geographic scales. Significant differences were detected in bacterial compositions between two study locations, Xishuangbanna and Hainan Island. Redundancy analysis showed that the most important factor driving bacterial composition was site location and total nitrogen, which explained 38.2 and 38.4% the total variance, respectively; this indicates that historical contingencies drive distinct bacterial communities in rubber plantation soils. At the local scale, there were also distinct differences in soil bacterial compositions between the dry and rainy season in both the Xishuangbanna and Hainan sites. Seasonal changes explained 13.6 and 41.4% of the total variation of soil bacterial composition in Xishuangbanna and on Hainan Island, respectively, whereas other factors had little effect on soil bacterial communities (p < 0.001). In conclusion, our results demonstrate that historical contingencies drive variation in bacterial composition at the geographic scale, whereas seasonal changes influence variation at the local scale.     

不同修复植被类型的三峡库区消落带土壤细菌群落分析

为了探究三峡库区消落带不同修复植被对土壤细菌群落结构的影响,以纯草地(A₁)、纯林地(A₂)和覆草林地(A₃)3种不同样地土壤为研究对象,采用土壤理化因子检测及扩增子测序的研究方法,分析了不同修复植被对三峡库区消落带土壤细菌群落的影响。结果表明:不同样地的pH值、全氮(TN)和全磷(TP)含量无显著性差异,A₁和A₃的土壤有机碳(SOC)含量之间无显著性差异,但均显著高于A₂(p<0.05); 相关分析显示样地土壤细菌群落ACE指数和Shannon指数与土壤SOC和TN含量显著正相关(p<0.05),Chao1指数与土壤SOC含量显著正相关(p<0.05); 不同样地土壤的细菌优势种群无明显区别; 属水平上6个优势种群的相对丰度与土壤SOC和TN含量显著相关(p<0.05); 冗余分析显示SOC是影响三峡库区消落带不同修复植被样地细菌群落的主要显著性因子(p<0.05)。由此可以得出,不同修复植被类型的消落带土壤的细菌优势种群无明显差异,土壤细菌群落结构主要受土壤SOC的影响。     

Changes of Bacterial Community Structure in Copper Mine Tailings After Colonization of Reed (Phragmites communis)

Soil samples were collected from both bare and vegetated mine tailings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed (Phragmites communis) colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic (pH = 3.78), whereas the vegetated mine tailing was near neutral (pH = 7.28). The contents of organic matter, total nitrogen, and ammonium acetate-extractable potassium in vegetated mine tailings were significantly higher than those in the bare mine tailings (P< 0.01), whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings (P< 0.01). The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.     

Parasitism by Cuscuta australis affects the rhizhospheric soil bacterial communities of Trifolium repens L.

ABSTRACT

The effect of parasitism on belowground microbial communities is not well understood. 16S rRNA gene amplicon sequencing was used to test the effect of Cuscuta australis parasitism on the composition and diversity of bacterial community in the rhizospheric soil of the host plant Trifolium repens. 94569 sequences were obtained from the amplicons of non-parasitised, and 97172 sequences were obtained from the parasitised rhizospheric soil bacterial community. Parasitism of C. australis significantly decreased the relative abundance of the bacterial phylum Nitrospirae, while it significantly increased that of Verrucomicrobia. Parasitism of C. australis significantly decreased the relative abundance of 10 bacterial genera, while it significantly increased those of nine genera. The Chao 1 indexes of the rhizospheric soil bacterial community of parasitised T. repens were significantly lower than those of non-parasitised T. repens. Principal coordinate analysis (based on the genus) and principal component analysis (based on the predicted gene function of bacterial communities) showed that rhizospheric bacterial communities from parasitised and non-parasitised T. repens differed and can be divided into two groups. These results suggest that infection of the holoparasitic plant could indirectly change the composition, diversity, and function of rhizospheric soil bacteria of the host plant.     

Bacterial communities associated with natural and commercially grown rooibos (Aspalathus linearis)

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea. Symbiotic interactions between A. linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor, acidic fynbos soil. The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A. linearis, as well as the effect of seasonal changes on these communities. Bacterial communities were characterized using high throughput amplicon sequencing, and their correlations with soil chemical properties were investigated. The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction. Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant bacterial phyla detected in this study. Highly similar bacterial communities were associated with natural and commercially grown plants. Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season, while no significant differences were detected in the wet season. This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A. linearis.     

Long term impact of mineral amendment on the distribution of the mineral weathering associated bacterial communities from the beech Scleroderma citrinum ectomycorrhizosphere

Liming is a known forest management procedure used to amend nutrient-poor soils such as soils of acidic forests to rectify cation deficiencies and to restore soil pH. However, although this procedure is well known for its beneficial effect on the forest trees, its relative impact on the functional and taxonomic diversity of the soil bacterial communities has been poorly investigated. In this study, we characterized the ability of the soil bacteria to weather soil minerals and to hydrolyze chitin. A collection of 80 bacterial strains was isolated from the Scleroderma citrinum ectomycorrhizosphere and the adjacent bulk soil in two stands of mature beeches (Fagus sylvatica) developed on very acidic soil and presenting two levels of calcium (Ca) availability: a control plot as well as a plot amended with Ca in 1973. All the bacterial isolates were identified by partial 16S rRNA gene sequence analysis as members of the genera Burkholderia, Bacillus, Dyella, Kitasatospora, Micrococcus, Paenibacillus, Pseudomonas, and Rhodanobacter. Using a microplate assay for quantifying the production of protons and the quantity of iron released from biotite, we demonstrated that the bacterial strains from the amended plot harbored a significant higher mineral weathering potential that the ones isolated from the control plot. Notably, the weathering efficacy of the ectomycorrhizosphere bacterial isolates was significantly greater than that of the bulk soil isolates in the control treatment but not in the amended plot. These data reveal that forest management, here mineral amendment, can strongly affect the structure of bacterial communities even over the long term.     

Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods

Viruses are highly abundant in temperate soils, ranging from 10⁷ to 10⁹?g^?1, and outnumbering soil bacteria from 5- to over 1,000-fold. In order to determine the potential impacts of viruses on soil microbial communities, it is important to establish reliable methods for comparing changes in viral abundances within and across soil samples. The goals of this study were to optimize extraction-enumeration methods to accurately determine viral abundances in a range of soil types, to evaluate the feasibility of simultaneously enumerating bacterial cells and virus particles using a single extraction procedure, and to assess the utility of flow cytometry (FCM) for enumerating virus particles in soil extracts. Comparisons of extraction approaches indicated that sonication or blender extraction of soils with potassium citrate buffer yielded the highest viral abundances for most soil types. Combined viral and bacterial extractions underestimate abundances compared to separately-optimized extractions for each. Flow cytometric counts were anywhere between 350- and 1,400-fold higher than epifluorescence microscopy (EFM)-based counts for the same soil. Trends in viral abundance across soil types were different from those via EFM, and different relationships between viral abundance and soil properties were observed depending on the enumeration method. Thus, FCM is not currently recommended for enumeration of viruses in soil extracts. Based on EFM results, soil moisture and organic matter content were the most important factors determining viral abundance in soils.     

氮肥水平对稻田细菌群落及N2O排放的影响

作为土壤氮素转化的驱动者,微生物群落结构关系着稻田氮素利用及温室气体N_2O排放等问题。本研究分别基于高通量测序和荧光定量PCR技术,分析了不同氮肥水平[CK(不施氮)、N(施N 180 kg·hm-2)、2/3N(施N 120 kg·hm-2)、1/3N(施N 60 kg·hm-2)]下稻田细菌群落及硝化反硝化关键微生物功能基因丰度的变化。结果显示:氮肥水平提高增加了稻田细菌物种丰富度Chao1指数和群落多样性Shannon指数,改变了细菌群落组成,其中与硝化作用相关的硝化螺菌门Nitrospirae和嗜酸的醋杆菌门Acidobacteria的相对丰度随氮肥水平提高而增加,但甲烷氧化菌Methylosinus的相对丰度随氮肥水平提高而降低。氮肥水平对稻田硝化作用关键微生物氨氧化细菌amo A基因丰度的影响较大,0~5 cm和10~20 cm深度土层中的amo A基因丰度均随氮肥用量增加而提高;反硝化作用关键微生物功能基因nir S、qno B和nos Z的丰度在不施肥处理(CK)中显著低于施肥处理(1/3N、2/3N和N)(P0.05),但1/3N、2/3N和N处理的稻田nir S基因丰度没有明显差异;0~5 cm土层中qno B和nos Z基因丰度存在随氮肥水平提高而增加的趋势,10~20 cm土层中nos Z基因丰度在2/3N和N处理下显著高于1/3N处理(P0.05)。N处理的稻田N_2O排放通量显著高于2/3N及1/3N处理(P0.05),后者又显著高于CK处理(P0.05)。相关分析结果表明稻田N_2O排放通量与0~5 cm土层中硝化螺菌门Nitrospirae相对丰度及10~20 cm土层中amo A基因丰度存在显著相关性(P0.05,n=10)。综上所述,氮肥水平提高增加了稻田细菌群落多样性,促进了稻田N_2O排放,且本研究稻田中硝化作用微生物群落及丰度变化与稻田N_2O排放的关系更为密切。     

Localization of atmospheric H2-oxidizing soil hydrogenases in different particle fractions of soil

Low atmospheric H₂ concentrations (0.55 ppmv) are oxidized in soils by a high-affinity activity with typical characteristics of an abiontic soil enzyme. This activity was measured in a meadow cambisol and a forest cambisol. In both soils, the maximum activity was reached at a soil moisture of about 20% water-holding capacity, and was localized in the top A_h horizon. The soils were fractionated by dry sieving and wet filtration into nine different particle-size fractions, ranging from 3 to 2000 m in size. H₂ oxidation was measured by three different assays and was compared to the ATP content and microscopic counts of bacteria in the same fractions. In the meadow soil, the specific activities of H₂ oxidation increased with the particle size (maximum at 200–500 m), whereas ATP and bacterial counts showed no trend. In the forest soil, the specific activities of H₂ oxidation increased with the particle size up to 50–100 m, and then decreased again. ATP and bacterial counts, however, showed the opposite trend, i.e., decreased with an increasing particle size. Thus the H₂-oxidizing activity was not correlated with characteristic microbial biomass parameters. Although significant percentage (29–64%) of randomly isolated heterotrophic bacteria was able to oxidize H₂, this activity was too small to account for the H₂ oxidation in the soil. In both soils, most of the activity present was found in particles of 100–500 m in size. The recovery shifted to smaller size fractions when larger soil aggregates were broken up by wet instead of dry sieving. Attempts to extract the H₂-oxidizing activity from the soil particles were unsuccessful.     

Dose-dependent effect of compost amendment on soil bacterial community composition and co-occurrence network patterns in soybean agroecosystem

ABSTRACT

This study aimed to elucidate the effects of various doses of compost amendment on bacterial community compositions and co-occurrence network patterns across the growing season in black soil, Northeast China. Bacterial richness was unaffected by compost addition in seedling and flowering stage, whereas significantly enhanced by high level of compost addition (45,000 kg ha^?1) in mature stage. Non-metric multidimensional scaling analysis revealed distinct bacterial communities in response to compost addition across the growing season. At phylum level, copiotrophic groups of bacteria including Bacteroidetes and Firmicutes gradually increased in relative abundance along with compost rate, while oligotrophic groups (Planctomycetes and Verrucomicrobia) showed opposite tendency. Notably, these enrichment or reduction was most pronounced in seedling stage. Abundant genera including Actinomadura, Aminobacter, Cellvibrio, Devosia, Luteimonas, Microbacterium, Nonomuraea, Promicromonospora were positively and consistently correlated with compost rate, whereas Arthrobacter, Flavisolibacter, Janthinobacterium, Kaistobacter negatively correlated. Network analysis indicated that compost amended soils (40.0, 49.0, and 64.0%) harbored more positive links than control (37.6%). In addition, the soil bacterial network connectivity and connectedness generally increased along with the compost rate, while modularity exhibited opposite trend. Overall, our findings show that compost addition modified the bacterial community compositions and network patterns in soybean agroecosystem in Northeast China.     

Sulfate treatment affects desulfonating bacterial community structures in Agrostis rhizospheres as revealed by functional gene analysis based on asfA

Sulfonates are major soil sulfur components that can be desulfurized by certain soil-borne bacteria as a sulfur source, but application of sulfate through fertilization could affect this natural sulfur mobilizing process. This study investigates the effects of sulfate treatments on bacterial communities in semi-natural grasslands. Agrostis stolonifera-dominated turfs with their autochthonous bacteria from Woburn Experimental Farm, UK, were incubated with and without additional sulfate over a period of eight weeks and compared to soil and rhizosphere samples taken from the field directly. Cultivable rhizobacteria able to desulfurize toluenesulfonate were dominated by strains affiliated to the Variovorax, Polaromonas and Rhodococcus genera. The betaproteobacteria communities (16S rRNA gene-based denaturing gradient gel electrophoresis) and the desulfonating bacterial communities (asfA based terminal restriction fragment length polymorphism) revealed clear differences between field rhizospheres and bulk soil and the two types of incubated rhizospheres. Clone libraries of asfA from the sulfate-limited treatment were dominated by a new AsfA type, affiliated to Polaromonas. The results from this study suggest that the community of desulfonating bacteria in the Agrostis rhizosphere adapts quickly to changing levels of inorganic sulfate.     

Bacterial communities in paddy soils changed by milk vetch as green manure: A study conducted across six provinces in South China

The use of green manures contributes to sustainable soil and nutrient management in agriculture; however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncertain. A study was undertaken across multiple sites and years in Hunan, Jiangxi, Anhui, Henan, Hubei, and Fujian provinces of South China to investigate the effects of green manuring on the structure and function of soil bacterial communities in rice-green manure cropping systems. The study included four treatments:winter fallow with no chemical fertilizer as a control (NF), milk vetch as green manure without chemical fertilizer (GM), winter fallow and chemical fertilizer (CF), and a combination of chemical fertilizer and milk vetch (GMCF). Significant differences were found in the responses of soil microbial communities at different sites, with sampling sites explaining 72.33% (F=36.59, P=0.001) of the community composition variation. The bacterial communities in the soils from Anhui, Henan, and Hubei were broadly similar, while those from Hunan were distinctly different from other locations. The analysis of Weighted UniFrac distances showed that milk vetch changed soil microbial communities compared with winter fallow. Proteobacteria and Chloroflexi predominated in these paddy soils; however, the application of green manures increased the relative abundance of Actinobacteria. There was evidence showing that the functional microbes which play important roles in the cycling of soil carbon, nitrogen (N), and sulfur (S) changed after several years of milk vetch utilization (linear discriminant analysis score > 2). The abundance of methane-oxidizing bacteria and S-reducing bacteria increased, and microbes involved in N fixation, nitrification, and denitrification also increased in some provinces. We concluded that the application of milk vetch changed the bacterial community structure and affected the functional groups related to nutrient transformation in soils at a regional scale.