Bacterial community structures in rhizosphere microsites of ryegrass (Lolium perenne var. Nui) as revealed by pyrosequencing

Management of soils to facilitate plant beneficial microbial interactions requires basic knowledge of the species composition and microbial community structures in the plant rhizosphere. Here, we examined composition of bacterial communities associated with rhizosphere microsites located at the root tips and mature root zones of Lolium perenne when grown in Chilean ash-derived volcanic soils (Andisols: Freire and Piedras Negras soil series). Community structures were analyzed by pyrosequencing of 16S ribosomal RNA (rRNA) genes followed by in silico analysis for phylogenetic assignments (MOTHUR and Visualization tool for Taxonomic Compositions of Microbial Community (VITCOMIC)). Analysis of the community structure revealed significant differences in community structures in relation to the soil series, which differed particularly in the relative abundance of Cyanobacteria and Firmicutes. However, no significant differences were observed with respect to root microsite location in the same Andisol series. Predominant taxa included members of the Proteobacteria, Actinobacteria, and Acidobacteria. Analysis by VITCOMIC showed that dominant bacterial groups comprised only 5 to 10 % of the total bacterial community and the remaining majority of bacteria included low-abundant taxa (Fusobacteria, Thermotogae, Lentisphaerae, Tenericutes, Deferribacteres Spirochaetes, Planctomycetes, Thermotogae, and Deinococcus-Thermus), most of which have not been previously reported or associated with the plant rhizosphere according to GenBank database. The results indicate that most of bacteria in the Chilean Andisols have not been described to the rhizosphere plants and their functional traits are still largely unknown.     

Influence of nitrogen fertilisation on pasture culturable rhizobacteria occurrence and the role of environmental factors on their potential PGPR activities

Plant growth-promoting rhizobacteria (PGPR) naturally occur in the rhizospheres of pasture, but still little is understood regarding how soil agricultural practices affect them. Here, we examined the effects of long-term nitrogen (N) fertilisation on the occurrence of potential culturable PGPR in rhizosphere soils from pastures grown in Chilean Andisols. We also evaluated in vitro the effects of organic acids (citric, malic and oxalic acids), metals (Al and Mn) and N supply (urea and ammonium sulphate) on indole acetic acid (IAA) production and phosphorus (P) liberation by selected strains. Compared with non-N-fertilised pasture, N fertilisation significantly increased (30%) the occurrence of culturable phosphobacteria but decreased (7%) the occurrence of IAA-producing rhizobacteria. Most efficient IAA-producing phosphobacteria were identified as Bacillus, Enterobacter, Pseudomonas and Serratia. At low pH (4.8), the assays showed that the IAA production by Serratia sp. N0-10LB was increased (31–74%) by organic acids. On the other hand, the IAA production by Pseudomonas sp. N1-55PA was increased two- to fivefold by metals. In all strains, the growth and IAA production were significant decreased by 500 μM of Al, except Serratia sp. N0-10LB, suggesting its potential as PGPR for Chilean Andisols. When urea was added as main N source, the bacterial growth and P utilisation significantly increased compared with ammonium sulphate. The influence of environmental factors that are typical of Chilean Andisols on rhizobacterial communities will provide better management practices to enhance their PGPR functions as well as a better selection biofertilisers to be used in Chilean Andisols.     

New processes of microbial transformation of nitrogen in soils as a source of greenhouse gases

DNA isolation from soil samples and amplification of fragment of a key gene of nitrification, archaeal and bacterial amoA, revealed presence of the product in all investigated soil samples. Characteristics of ammonia-oxidizing microbial communities in agrocenoses and undisturbed soil were determined. Bacteria were predominant in agrocenoses (at circum-neurtal pH), whereas the share of representatives of domain Archaea (phylum Thaumarchaeota) increased in prokaryotic ammonia-oxidizing complexes of undisturbed forest ecosystems (at low pH). It was demonstrated that the contribution of taumarhaea in nitrous oxide emission from gray forest soil may reach 20–25%.     

Bacterial Community Composition and Genes for Herbicide Degradation in a Stormwater Wetland Collecting Herbicide Runoff

Stormwater wetlands collect and attenuate runoff-related herbicides, limiting their transport into aquatic ecosystems. Knowledge on wetland bacterial communities with respect to herbicide dissipation is scarce. Previous studies showed that hydrological and hydrochemical conditions, including pesticide removal capacity, may change from spring to summer in stormwater wetlands. We hypothesized that these changes alter bacterial communities, which, in turn, influence pesticide degradation capacities in stormwater wetland. Here, we report on bacterial community changes in a stormwater wetland exposed to pesticide runoff, and the occurrence of trz, atz, puh, and phn genes potentially involved in the biodegradation of simazine, diuron, and glyphosate. Based on T-RFLP analysis of amplified 16S rRNA genes, a response of bacterial communities to pesticide exposure was not detected. Changes in stormwater wetland bacterial community mainly followed seasonal variations in the wetland. Hydrological and hydrochemical fluctuations and vegetation development in the wetland presumably contributed to prevent detection of effects of pesticide exposure on overall bacterial community. End point PCR assays for trz, atz, phn, and puh genes associated with herbicide degradation were positive for several environmental samples, which suggest that microbial degradation contributes to pesticide dissipation. However, a correlation of corresponding genes with herbicide concentrations could not be detected. Overall, this study represents a first step to identify changes in bacterial community associated with the presence of pesticides and their degradation in stormwater wetland.     

Endophytic bacteria from selenium-supplemented wheat plants could be useful for plant-growth promotion,biofortification and Gaeumannomyces graminis biocontrol in wheat production

In this study, we isolated putative plant-growth-promoting endophytic bacteria from selenium-supplemented wheat grown under field conditions. These bacterial strains belonged to Bacillus, Paenibacillus, Klebsiella, and Acinetobacter genera and showed genetic similarly with rhizospheric bacteria isolated in the same Andisol soil and with other endophytic strains previously reported. Strains isolated from selenium-supplemented wheat were highly tolerant to elevated selenium concentration (ranged from 60 to 180 mM), and showed potential plant-growth-promoting capabilities (auxin and siderophore production, phytate mineralization, and tricalcium phosphate solubilization). In addition, some strains like Acinetobacter sp. (strain E6.2), Bacillus sp. (strain E8.1), Bacillus sp., and Klebsiella sp. (strains E5 and E1) inhibited the growth of Gaeumannomyces graminis mycelia in vitro at 100, 50, and 30 %, respectively. These endophytic microorganisms would be useful for dual purposes: selenium biofortification of wheat plants and control of G. graminis, the principal soil-borne pathogen in volcanic soils from southern Chile.     

Chemical nature of soil organic carbon under different long-term fertilization regimes is coupled with changes in the bacterial community composition in a Calcaric Fluvisol

Fertilization is an important factor influencing the chemical structure of soil organic carbon (SOC) and soil microbial communities; however, whether any connection exists between the two under different fertilization regimes remains unclear. Soils from a 27-year field experiment were used to explore potential associations between SOC functional groups and specific bacterial taxa, using quantitative multiple cross-polarization magic-angle spinning ¹³C nuclear magnetic resonance and 16S rRNA gene sequencing. Treatments included balanced fertilization with organic materials (OM) and with nitrogen (N), phosphorus (P), and potassium (K) mineral fertilizers (NPK); unbalanced fertilization without one of the major elements (NP, PK, or NK); and an unamended control. These treatments were divided into four distinct groups, namely OM, NPK, NP plus PK, and NK plus control, according to their bacterial community composition and SOC chemical structure. Soil total P, available P, and SOC contents were the major determinants of bacterial community composition after long-term fertilization. Compared to NPK, the OM treatment generated a higher aromatic C–O and OCH₃ and lower alkyl C and OCH abundance, which were associated with the enhanced abundance of members of the Acidobacteria subgroups 6 and 5, Cytophagaceae, Chitinophagaceae, and Bacillus sp.; NP plus PK treatments resulted in a higher OCH and lower aromatic C–C abundance, which showed a close association with the enrichment of unclassified Chloracidobacteria, Syntrophobacteraceae, and Anaerolineae and depletion of Bacillales; and NK plus control treatments resulted in a higher abundance of aromatic C–C, which was associated with the enhanced abundance of Bacillales. Our results indicate that different fertilization regimes changed the SOC chemical structure and bacterial community composition in different patterns. The results also suggest that fertilization-induced variations in SOC chemical structure were strongly associated with shifts in specific microbial taxa which, in turn, may be affected by changes in soil properties.     

Antifungal and Plant Growth Promoting Activities of Indigenous Rhizobacteria Isolated from Maize (Zea mays L.) Rhizosphere

Plant growth promoting rhizobacteria (PGPR) enhance the plant growth directly by assisting in nutrient acquisition and modulating plant hormone levels, or indirectly by decreasing the inhibitory effects of various pathogens. The aim of this study was to select effective PGPR from a series of indigenous bacterial isolates by plant growth promotion and antifungal activity assays. This study confirmed that most of the isolates from maize rhizosphere were positive for PGPR properties by in vitro tests. Azotobacter and Bacillus isolates were better phosphate solubilizers and producers of lytic enzymes, hydrocyanic acid (HCN), and siderophores than Pseudomonas. Production of indole-3-acetic acid (IAA) and antifungal activity were the highest in Azotobacter, followed by Bacillus and Pseudomonas. The most effective Azotobacter isolates (Azt₃, Azt₆, Azt₁₂) and Bacillus isolates (Bac_10, Bac₁₆) could be used as PGPR agents for improving maize productivity. Further selection of isolates will be necessary to determine their efficiency in different soils.     

Antibiotic resistant coliform and faecal coliform bacteria in drinking water

Coliform and faccal coliform were isolated from drinking water samples obtained from tap water (TW) and storage tanks (ST) in Baghdad city. All isolates were identified and tested for their resistance to twelve antibiotics. Bacterial identification revealed that Ent. cloacae and Kl. pneumoniae were the predominant organisms from TW and ST water samples, respectively. Overall, 66% of the isolates from TW and 38% from ST were resistant to one or more of the drugs tested. Ampicillin, Carbenicillin, Cefalotin and Colistin resistance in particular were more frequent among bacterial isolates. The overall frequency of multiple antibiotic resistance among bacterial isolates in TW and ST samples were 47% and 33%, respectively. All bacterial strains isolated from drinking water were sensitive to Rifampicin. Results demonstrated the need for periodical bacteriological examination of drinking water and restriction in the use of antibiotics in this country.     

Forest soil community responses to plant growth-promoting rhizobacteria and spruce seedlings

The influence of plant-growth-promoting rhizobacteria (PGPR) and spruce seedlings on the composition and activity of forest soil microbial communities was studied in a microcosm experiment in which sterile, sand-filled 25mm×150mm glass tubes were treated with a forest soil suspension containing Bacillus or Pseudomonas PGPR and 2-week-old spruce seedlings. Eighteen weeks after treatments were established, bacterial, actinomycete and fungal population sizes were determined by dilution plating, as were seedling dry weights and soil carbon substrate utilization profiles using Biolog plates. PGPR inoculation had little influence on the population sizes of actinomycetes or fungi. However, significant effects were detected on the total bacterial population size, primarily in microcosms without seedlings. Euclidean distances between treatments plotted on two dimensions by multidimensional scaling showed that the introduction of PGPR strains changed the type of microbial community, particularly when inoculated into soil without seedlings. Significant changes were also detected in one soil type in the presence of seedlings. Our results suggest that the type of soil community and the presence of seedlings are significant factors influencing the responses of soil communities to bacterial inoculation, and that for some soil communities, the presence of seedlings may mitigate perturbations caused by the introduction of PGPR. Received: 24 February 1997     

Characteristics of bacterial community in the water and surface sediment of the Yellow River,China, the largest turbid river in the world

Purpose

Few studies have described the bacterial community structures of turbid rivers. In this paper, the characteristics of the bacterial community in the water and surface sediment of the Yellow River, China, the largest turbid river in the world, were studied.

Materials and methods

Water and sediment samples were collected from six sites along the river. Bacterial community composition was determined using the 16S ribosomal RNA (rRNA) gene clone library technique. The relationship between environmental parameters and bacterial diversity was analyzed.

Results and discussion

A total of 1,131 gene sequences were obtained and clustered into 639 operational taxonomic units (at the 97 % identity level), with Proteobacteria as the predominant phylum. The Shannon index for water samples ranged from 3.39 to 4.40 and was generally higher than that in other rivers; this was probably due to the high suspended particulate sediment (SPS) concentration in the Yellow River, which can provide more habitats for both aerobic and anaerobic bacteria. Also, the bacterial diversity of the water samples was slightly higher than that of the surface sediment samples. The bacterial diversity of water increased along the river in the downstream direction, while there was no trend for the sediment. Redundancy analysis indicated that pH, dissolved organic carbon (DOC), and SPS were the main factors controlling the water bacterial community in the Yellow River, and pH, nitrate–nitrogen, and water content were the main factors for the surface sediment bacterial community.

Conclusions

This study indicated that the bacterial diversity of the Yellow River is generally higher than that in other rivers, suggesting that SPS plays an important role in regulating bacterial diversity and community structure in aquatic environments.     

Plant growth stage, fertiliser management and bio-inoculation of arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria affect the rhizobacterial community structure in rain-fed wheat fields

The goal of this study was first to assess the dynamics of the bacterial community during a growing season in three Indian rain-fed wheat fields which differ mainly through their fertilizer management and yield and then to study the effects of PGPR/AMF bio-inoculations on the bacterial community structure and wheat growth. The bacterial community structure of the rhizosphere soil (RS) and the rhizoplane/endorhizosphere (RE) was determined by PCR-denaturing gradient gel electrophoresis. Seed treatments consisted of consortia of two PGPR strains alone or combined with AMF or AMF alone. The PGPR strains were Pseudomonas spp. which included some or all of the following plant growth promoting properties: phosphate solubilisation and production of indole-3-acetic acid, siderophores, 1-aminocyclopropane-1-carboxylate deaminase and diacetyl-phloroglucinol. The mycorrhizal inoculum was an indigenous AMF consortium isolated from the field with the lowest level of fertilization and yield. Variation partitioning analysis of the DGGE data indicated a predominant effect of the wheat growth stage (30.4% of the variance, P=0.001) over the type of field (9.0%, P=0.027) on the bacterial community structure in the RE. The impact of plant age in the RS was less than in the RE and the bacterial community structure of the field with the highest input of fertilization was very different from the low input fields. The bio-inoculants induced a significant modification in the bacterial community structure. In the RS, the bacterial consortia explained 28.3% (P=0.001) and the presence of AMF 10.6% (P=0.02) of the variance and the same trend was observed in the RE. Plant yield or grain quality was either increased or remained unaffected. For example, protein content was significantly higher in the treated plants' grain compared to the control plants; maximum values were obtained when the PGPR were co-inoculated with the AMF. The percentage of root colonization by AMF was significantly higher in the treatments containing a mycorrhizal inoculum than in the untreated control and remained unaffected by the PGPR treatments. In conclusion, the wheat rhizobacterial community structure is highly dynamic and influenced by different factors such as the plant's age, the fertilizer input and the type of bio-inoculant. In addition, there is a distance-related effect of the root on the bacterial community. Finally, a combined bio-inoculation of diacetyl-phloroglucinol producing PGPR strains and AMF can synergistically improve the nutritional quality of the grain without negatively affecting mycorrhizal growth.     

Shift in abundance and structure of soil ammonia-oxidizing bacteria and archaea communities associated with four typical forest vegetations in subtropical region

Purpose

Nitrogen (N) is one of the most important elements that can limit plant growth in forest ecosystems. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global N biogeochemical cycling. Soil ammonia-oxidizing microbial communities associated with subtropical vegetation remain poorly characterized. The aim of this study was to determine how AOA and AOB abundance and community structure shift in response to four typical forest vegetations in subtropical region.

Materials and methods

Broad-leaved forest (BF), Chinese fir forest (CF), Pinus massoniana forest (PF), and moso bamboo forest (MB) were widely distributed in the subtropical area of southern China and represented typical vegetation types. Four types of forest stands of more than 30 years grew adjacent to each other on the same soil type, slope, and elevation, were chosen for this experiment. The abundance and community structure of AOA and AOB were characterized by using real-time PCR and denaturing gradient gel electrophoresis (DGGE). The impact of soil properties on communities of AOA and AOB was tested by canonical correspondence analysis (CCA).

Results and discussion

The results indicated that AOB dominated in numbers over AOA in both BF and MB soils, while the AOA/AOB ratio shifted with different forest stands. The highest archaeal and bacterial amoA gene copy numbers were detected in CF and BF soils, respectively. The AOA abundance showed a negative correlation with soil pH and organic C but a positive correlation with NO₃ ^??N concentration. The structures of AOA communities changed with vegetation types, but vegetation types alone would not suffice for shaping AOB community structure among four forest soils. CCA results revealed that NO₃ ^??N concentration and soil pH were the most important environmental gradients on the distribution of AOA community except vegetation type, while NO₃ ^??N concentration, soil pH, and organic C significantly affected the distribution of the AOB communities.

Conclusions

These results revealed the differences in the abundance and structure of AOA and AOB community associated with different tree species, and AOA was more sensitive to vegetation and soil chemical properties than AOB. N bioavailability could be directly linked to AOA and AOB community, and these results are useful for management activities, including forest tree species selection in areas managed to minimize N export to aquatic systems.     

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana <Emphasis Type="Italic">Fusarium</Emphasis> wilt disease by reshaping the soil microbiome

Two seasonal pot experiments were conducted to investigate the effect of biofertilizer application after mixture of lime and ammonium bicarbonate (LA) fumigation, on banana Fusarium wilt disease suppression and soil microbial community composition. Biofertilizer application after LA fumigation decreased 80% of disease incidence compared to control of biofertilizer application to non-fumigated soil. Biofertilizer application after fumigation clearly manipulated soil microbial community composition as revealed by non-metric multidimensional scaling and Venn diagram. LA fumigation significantly reduced the abundance of F. oxysporum while biofertilizer application after fumigation could further decrease it. Furthermore, indigenous microbes, e.g., Bacillus, Pseudomonas, and Mortierella, were associated with disease suppression. Biofertilizer application after fumigation significantly (p?<?0.05) increased the soil pH and content of soil total C and available P and K, and this probably reshaped soil microbial community as revealed by redundancy analysis and variance partitioning analysis. The observed disease suppression due to biofertilizer application after soil fumigation can be attributed to the reduced abundance of F. oxysporum by general suppression resulting from manipulated soil properties and recovered soil microbiome.     

Soil microbial abundance and community structure vary with altitude and season in the coniferous forests,China

Purpose

Soil microbes control the bioelement cycles and energy transformation in forest ecosystems, and are sensitive to environmental change. As yet, the effects of altitude and season on soil microbes remain unknown. A 560 m vertical transitional zone was selected along an altitude gradient from 3023, 3298 and 3582 m, to determine the potential effects of seasonal freeze-thaw on soil microbial community.

Materials and methods

Soil samples were collected from the three elevations in the growing season (GS), onset of freezing period (FP), deeply frozen period (FPD), thawing period (TP), and later thawing period (TPL), respectively. Real-time qPCR and polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) were used to measure the abundance and structure of soil microbial community.

Results and discussion

The bacterial, archaeal, and fungal ribosomal DNA (rDNA) copy numbers decreased from GS to freezing stage (FP and FPD) and then increased in thawing stage (TP and TPL). Similarly, the diversity of microbial community varied with seasonal freeze-thaw processes. The diversity index (H) of the bacterial and archaeal communities decreased from GS to FP and then increased to TPL. The fungal community H index increased in the freezing process.

Conclusions

Our results suggested that abundance and structure of soil microbial community in the Tibetan coniferous forests varied by season and bacterial and archaeal communities respond more promptly to seasonal freeze-thaw processes relative to fungal community. This may have important implications for carbon and nutrient cycles in alpine forest ecosystems. Accordingly, future warming-induced changes in seasonal freeze-thaw patterns would affect soil nutrient cycles via altering soil microbial properties.

     

Long-term agronomic practices alter the composition of asymbiotic diazotrophic bacterial community and their nitrogen fixation genes in an acidic red soil

The asymbiotic diazotrophic bacteria are important for nitrogen (N) input to soil. Here, we investigated asymbiotic diazotrophic bacteria in an acidic red soil from functional, phylogenetic, and ecological perspectives. We firstly confirmed that phosphorus (P) availability determines the overall asymbiotic N fixation potential in the red soil. Then, we analyzed the soil bacterial community and N fixing (nifH) gene composition. Long-term different fertilizations significantly affected the composition of soil bacterial community. In addition, long-term organic cultivations increased most of the asymbiotic diazotrophic bacteria and the corresponding nifH gene abundances. Few asymbiotic diazotrophic bacteria, belonging to Chloroflexaceae, Methylocystaceae, Enterobacteriaceae, and Pseudomonadaceae, and their corresponding nifH genes were more abundant in N and P co-limited than in not co-limited soils, suggesting that some bacterial taxa from these families might be activated under nutrient limited conditions. Our findings provided new information for the distribution of asymbiotic diazotrophic bacteria in red soil and gave insights into the ecology of diazotrophic bacteria.     

Altered precipitation seasonality impacts the dominant fungal but rare bacterial taxa in subtropical forest soils

How soil microbial communities respond to precipitation seasonality change remains poorly understood, particularly for warm-humid forest ecosystems experiencing clear dry-wet cycles. We conducted a field precipitation manipulation experiment in a subtropical forest to explore the impacts of reducing dry-season rainfall but increasing wet-season rainfall on soil microbial community composition and enzyme activities. A 67% reduction of throughfall during the dry season decreased soil water content (SWC) by 17–24% (P < 0.05), while the addition of water during the wet season had limited impacts on SWC. The seasonal precipitation redistribution had no significant effect on the microbial biomass and enzyme activities, as well as on the community composition measured with phospholipid fatty acids (PLFAs). However, the amplicon sequencing revealed differentiated impacts on bacterial and fungal communities. The dry-season throughfall reduction increased the relative abundance of rare bacterial phyla (Gemmatimonadetes, Armatimonadetes, and Baoacteriodetes) that together accounted for only 1.5% of the total bacterial abundance by 15.8, 40, and 24% (P < 0.05), respectively. This treatment also altered the relative abundance of the two dominant fungal phyla (Basidiomycota and Ascomycota) that together accounted for 72.4% of the total fungal abundance. It increased the relative abundance of Basidiomycota by 27.4% while reduced that of Ascomycota by 32.6% (P < 0.05). Our results indicate that changes in precipitation seasonality can affect soil microbial community composition at lower taxon levels. The lack of community-level responses may be ascribed to the compositional adjustment among taxonomic groups and the confounding effects of other soil physicochemical variables such as temperature and substrate availability.     

Abundance and community structure of ammonia oxidizing bacteria and archaea in a Sweden boreal forest soil under 19-year fertilization and 12-year warming

Purpose

Boreal forests are considered to be more sensitive to global climate change compared with other terrestrial ecosystems, but the long-term impact of climate change and forest management on soil microbial functional diversity is not well understood. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the most important players in nitrogen (N) cycling-associated processes in terrestrial ecosystems. This study investigated the separate and combined impacts of long-term soil warming and fertilization on soil AOB and AOA community structures and abundances in a Norway spruce stand in northern Sweden.

Materials and methods

The soil-warming experiment was established in the buffer zones of two irrigated plots (I) and complete nutrient solution plots (IL) since 1995. The warming treatment started in April each year by maintaining soil temperature on warmed plots at 5°C above the temperature in unwarmed plots using heating cables. In August 2006, soil samples were collected from eight subplots for molecular analysis. The abundance of bacterial and archaeal amoA genes was determined by quantitative polymerase chain reaction. Similarly, total bacterial and archaeal population sizes have also been determined. The diversity of AOB and AOA was assessed by constructing amoA gene clone libraries, and different genotypes were screened with restriction fragment length polymorphism.

Results and discussion

Results showed that fertilization did not significantly affect the abundance of the bacterial amoA gene under either warming or non-warming conditions; however, warming decreased the abundance under fertilization treatments. No significant effects of fertilization and soil warming were observed on the number of thaumarchaeal amoA gene copies across all treatments. In this study, amoA gene abundance of AOB was significantly higher than that of AOA across all treatments. The community structure of both AOB and AOA was strongly influenced by fertilization. For bacterial amoA genes, Nitrosospira cluster 2 was present across all treatments, but the only genotype was observed in the fertilization treatments while, for thaumarchaeal amoA genes, the relative abundance of soil cluster 5 increased in fertilization treatments. By comparison, soil-warming effects on AOB and AOA community structure were not significant. Canonical correspondence analysis showed a positive correlation between fertilization and both dominant genotypes of AOB and AOA.

Conclusions

These results indicated that the abundance of AOA and AOB was not affected by fertilization or warming alone, but the interaction of fertilization and warming reduced the abundance of AOB. The community composition of ammonia-oxidizers was more affected by the nutrient-optimized fertilization than the soil warming.     

Influence of Physicochemical Factors on Bacterial Communities Along the Lower Mekong River Assessed by Illumina Next-Generation Sequencing

The relationship between land use and microbial community structure at seven sites along the Lower Mekong River, between Thailand and the Loa People’s Democratic Republic, was investigated using Illumina next-generation sequencing of the V5–V6 hypervariable regions of the 16S rRNA gene. In total, 14,470 operational taxonomic units (OTUs) were observed. Community composition was significantly different between sampling years. Moraxellaceae and Comamonadaceae were the predominant bacterial families in upstream sites, which included agricultural and urban areas in the Loei and Nong Khai provinces of Thailand. Members of the family Comamonadaceae were prevalent in agricultural and urban sites in Bueng Kan Province, while Moraxellaceae and Burkholderiaceae were the major families in a site downstream of an urban area in the Nakhon Phanom Province of Thailand. The bacterial community observed from a forested area of Patam National Park in Thailand showed greatest diversity, and several major bacterial families including Comamonadaceae, Moraxellaceae, and Pseudomonadaceae were more dominant than other sites. The diversity of fecal indicator bacteria, determined by ERIC-PCR DNA fingerprinting, indicated the presence of 29 strains of Escherichia coli and 21 strains of Enterococcus, while TP-RAPD patterns represented six species of Enterococcus. Results of this study indicated that although the difference in the distribution of bacterial phyla and families was found among sampling sites, the bacterial community composition, based on the presence of OTUs, continuously retained its signature across approximately 758 km along the Lower Mekong River, regardless of the type of land use. Water parameters, including temperature, turbidity, DO, and air temperature, also differentially affected the abundance of bacterial families along the Mekong River.     

Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients

Purpose

Rhizosphere soil bacterial communities are crucial to plant growth, health, and stress resistance. In order to detect how bacterial communities associated with the rhizosphere of phylogenetically related plant species vary in terms of composition, function, and diversity, we investigated the rhizosphere bacterial community structure of two perennial shrub species, Caragana jubata and Caragana roborovskyi, under natural field conditions in northwest China and analyzed the influence of soil properties and environmental factors.

Materials and methods

Eighteen root samples, eight for C. jubata, and ten for C. roborovskyi, along with any adherent soil particles, were collected from multiple sites in northwest China. The rhizosphere soil was washed from the roots, and bacterial communities were analyzed using Illumina MiSeq sequencing of 16S rRNA gene amplicons. Then, α-diversity and β-diversity were calculated using QIIME.

Results and discussion

Across species, Proteobacteria (29 %), Actinobacteria (15 %), Chloroflexi (10 %), Acidobacteria (10 %), Bacteroidetes (8 %), Firmicutes (8 %), Planctomycetes (7 %), Gemmatimonadetes (4 %), and Verrucomicrobia (3 %) were the most abundant phyla in the rhizosphere of C. jubata and C. roborovskyi. However, principal co-ordinates analysis indicated strong interspecific patterns of bacterial rhizosphere communities. Further, the richness of Proteobacteria, Acidobacteria, Bacteroidetes, Verrucomicrobia, Firmicutes, and Nitrospirae was significantly higher in the rhizosphere of C. jubata compared with C. roborovskyi, while the opposite was found for Actinobacteria and Cyanobacteria. However, the Shannon index showed no significant difference in α-diversity between C. jubata and C. roborovskyi. Distance-based redundancy analysis indicated that soil properties and environmental factors exerted strong influences on the structure of the rhizosphere bacterial community and explained 47 and 46 % of community variances between samples, respectively.

Conclusions

Our results showed strong interspecific clustering of the bacterial rhizosphere communities of C. roborovskyi and C. jubata. Altitude explained most of the variation in the composition of bacterial rhizosphere communities of C. roborovskyi and C. jubata, followed by soil pH, water content, organic matter content, total nitrogen content, and mean annual rainfall.

     

在受控条件下植物促生菌对扁豆的生长，结瘤和养分积累的效应

Application of plant growth-promoting rhizobacteria (PGPR) has been shown to increase legume growth and development under field and controlled environmental conditions. The present study was conducted to isolate plant growth-promoting rhizobacteria (PGPR) from the root nodules of lentil (Lens culinaris Medik.) grown in arid/semi-arid region of Punjab, Pakistan and examined their plant growth-promoting abilities. Five bacterial isolates were isolated, screened in vitro for plant growth-promoting (PGP) characteristics and their effects on the growth of lentil were assessed under in vitro, hydroponic and greenhouse (pot experiment) conditions. All the isolates were Gram negative, rod-shaped and circular in form and exhibited the plant growth-promoting attributes of phosphate solubilization and auxin (indole acetic acid, IAA) production. The IAA production capacity ranged in 0.5-11.0 μg mL-1 and P solubilization ranged in 3-16 mg L-1 . When tested for their effects on plant growth, the isolated strains had a stimulatory effect on growth, nodulation and nitrogen (N) and phosphorus (P) uptake in plants on nutrient-deficient soil. In the greenhouse pot experiment, application of PGPR significantly increased shoot length, fresh weight and dry weight by 65%, 43% and 63% and the increases in root length, fresh weight and dry weight were 74%, 54% and 92%, respectively, as compared with the uninoculated control. The relative increases in growth characteristics under in vitro and hydroponic conditions were even higher. PGPR also increased the number of pods per plant, 1 000-grain weight, dry matter yield and grain yield by 50%, 13%, 28% and 29%, respectively, over the control. The number of nodules and nodule dry mass increased by 170% and 136%, respectively. After inoculation with effective bacterial strains, the shoot, root and seed N and P contents increased, thereby increasing both N and P uptake in plants. The root elongation showed a positive correlation (R2 = 0.67) with the IAA production and seed yield exhibited a positive correlation (R2 = 0.82) with root nodulation. These indicated that the isolated PGPR rhizobial strains can be best utilized as potential agents or biofertilizers for stimulating the growth and nutrient accumulation of lentil.