供磷水平和根际效应协同影响含碱性磷酸酶基因细菌群落的网络复杂性和稳定性北大核心

【目的】通过研究长期不同供磷水平下根际、土体土壤中编码碱性磷酸酶基因(alkaline phosphatase gene,phoD)细菌群落特征、网络复杂性、群落的稳定性及其与磷酸酶活性之间的关系,揭示供磷水平和根际效应在调控土壤有机磷矿化中的微生物学机制。【方法】选取华北平原长期施磷的小麦-玉米轮作体系石灰性土壤为基质土壤,开展根箱试验。选取的试验处理包括3个供磷水平,分别是0、50.0、200.0 kg P/hm^(2)(分别表示为P0、P50、P200)。玉米种子播种30 d后,采集玉米的根际土和土体土。采用高通量测序技术分析根际和土体土壤中编码碱性磷酸酶基因(phoD)细菌群落,探究施肥及根际效应对含phoD基因细菌的群落特征、网络特征的影响及其与磷酸酶活性的关系。【结果】随着施磷量的增加,速效磷(available P,AP)和碱性磷酸酶(alkaline phosphatase,ALP)活性在根际、土体土壤中均显著提高,且两者呈显著正相关。phoD基因丰度在P0、P200处理的根际土壤中显著高于土体土壤。含phoD基因细菌群落的α多样性在P50处理下的根际土壤显著高于土体土壤。冗余分析(redundancy analysis,RDA)表明,土壤中AP、有机磷(organic P,Po)和全磷(total P,Pt)是影响微生物群落的主要因素。与不施磷处理(P0)相比,施磷处理(P50、P200)下根际土壤中网络节点数和连接数降低,而土体土壤中网络节点数和连接数增加;同时,施磷处理含phoD基因细菌群落的鲁棒性(robustness)在根际土壤中显著提高,而在土体土壤中显著降低。Mantel检验表明,含phoD基因微生物群落中的优势物种在根际土壤与AP、酸性磷酸酶(acid phosphatase,ACP)、内聚力(cohesion)和网络的鲁棒性显著相关,在土体土壤中无显著性。【结论】供磷水平及根际效应协同影响phoD基因丰度、含phoD基因细菌群落的α多样性、群落结构、优势物种、网络的复杂性及群落的稳定性,进而影响磷酸酶活性,调控了土壤中有机磷的矿化。     

Cloning,sequencing and characterization of the alkaline phosphatase gene (phoD) from Zymomonas mobilis

The phoD gene encoding the membrane-bound alkaline phosphatase (ALPI) from Zymomonas mobilis CP4 was cloned and sequenced. Both the translated sequence and the properties of the recombinant enzyme were unusual. Z. mobilis ALPI was monomeric (_r 62926) and hydrolysed nucleotides more effectively than sugar phosphates. The translated sequence contained a single hydrophobic segment near the N-terminus which may serve as a membrane-anchor in Z. mobilis, although the recombinant enzyme was recovered in the cytoplasmic fraction of Escherichia coli. The predicted amino acid sequence for ALPI did not align well with other ALPs or other known genes. However, some similarity to E. coli ALP was noted in the metal-binding and phosphate-binding regions. Two other regions were identified with similarity to the active sites of pyruvate kinase and mammalian 5′-nucleotide phosphodiesterase (also membrane-bound), respectively. It is likely that Z. mobilis phoD represents a new class of alkaline phosphatase genes which has not been described previously.     

PCR Primers That Amplify Fungal rRNA Genes from Environmental Samples

Two PCR primer pairs were designed to amplify rRNA genes (rDNA) from all four major phyla of fungi: Ascomycota, Basidiomycota, Chytridomycota, and Zygomycota. PCRs performed with these primers showed that both pairs amplify DNA from organisms representing the major taxonomic groups of fungi but not from nonfungal sources. To test the ability of the primers to amplify fungal rDNA from environment samples, clone libraries from two avocado grove soils were constructed and analyzed. These soils possess different abilities to inhibit avocado root rot caused by Phythophthora cinnamomi. Analysis of the two rDNA clone libraries revealed differences in the two fungal communities. It also revealed a markedly different depiction of the soil fungal community than that generated by a culture-based analysis, confirming the value of rDNA-based approaches for identifying organisms that may not readily grow on agar media. Additional evidence of the usefulness of the primers was obtained by identifying fungi associated with avocado leaves. In both the soil and leaf analyses, no nonfungal rDNA sequences were identified, illustrating the selectivity of these PCR primers. This work demonstrates the ability of two newly developed PCR primer sets to amplify fungal rDNA from soil and plant tissue, thereby providing unique tools to examine this vast and mostly undescribed community of organisms.     

Land‐use influences phosphatase gene microdiversity in soils

Phosphorus cycling exerts significant influence upon soil fertility and productivity – processes largely controlled by microbial activity. We adopted phenotypic and metagenomic approaches to investigate phosphatase genes within soils. Microbial communities in bare fallowed soil showed a marked capacity to utilise phytate for growth compared with arable or grassland soil communities. Bare fallowed soil contained lowest concentrations of orthophosphate. Analysis of metagenomes indicated phoA, phoD and phoX, and histidine acid and cysteine phytase genes were most abundant in grassland soil which contained the greatest amount of NaOH‐EDTA extractable orthophosphate. Beta‐propeller phytase genes were most abundant in bare fallowed soil. Phylogenetic analysis of metagenome sequences indicated the phenotypic shift observed in the capacity to mineralise phytate in bare fallow soil was accompanied by an increase in phoD, phoX and beta‐propeller phytase genes coding for exoenzymes. However, there was a remarkable degree of genetic similarity across the soils despite the differences in land‐use. Predicted extracellular ecotypes were distributed across a greater range of soil structure than predicted intracellular ecotypes, suggesting that microbial communities subject to the dual stresses of low nutrient availability and reduced access to organic material in bare fallowed soils rely upon the action of exoenzymes.     

Diverse responses of pqqC- and phoD-harbouring bacterial communities to variation in soil properties of Moso bamboo forests

Phosphate-mobilizing bacteria (PMB) play a critical role in the regulation of phosphorus availability in the soil. The microbial genes pqqC and phoD encode pyrroloquinoline quinone synthase and bacterial alkaline phosphatase, respectively, which regulate inorganic and organic phosphorus mobilization, and are therefore used as PMB markers. We examined the effects of soil properties in three Moso bamboo forest sites on the PMB communities that were profiled using high-throughput sequencing. We observed differentiated responses of pqqC- and phoD-harbouring PMB communities to various soil conditions. There was significant variation among the sites in the diversity and structure of the phoD-harbouring community, which correlated with variation in phosphorus levels and non-capillary porosity; soil organic carbon and soil water content also affected the structure of the phoD-harbouring community. However, no significant difference in the diversity of pqqC-harbouring community was observed among different sites, while the structure of the pqqC-harbouring bacteria community was affected by soil organic carbon and soil total nitrogen, but not soil phosphorus levels. Overall, changes in soil conditions affected the phoD-harbouring community more than the pqqC-harbouring community. These findings provide a new insight to explore the effects of soil conditions on microbial communities that solubilize inorganic phosphate and mineralize organic phosphate.     

Distribution of alkaline phosphatase genes in cyanobacteria and the role of alkaline phosphatase on the acquisition of phosphorus from dissolved organic phosphorus for cyanobacterial growth

Phosphorus is a vital nutrient for cyanobacterial growth. Aside from dissolved inorganic phosphorus, dissolved organic phosphorus (DOP) is used by cyanobacterial species via the activity of alkaline phosphatase (APase), which likely plays an important role in acquiring phosphorus for algal growth in the same manner as it does in other bacteria. In this work, APase genes phoA, phoD, and phoX were found distributed in the cyanobacterial strains included in the algal genome collection of the NCBI database. PhoX has a wider distribution than the classical phoA and phoD. Furthermore, multiple types of APase genes were simultaneously identified in a single strain or genome. Anabaena flos-aquae FACHB-245 was selected as a typical strain to study the performance of cyanobacteria growing on DOP. In algal growth involving AMP or lecithin, APase regulates the release of phosphorus from DOP as confirmed by the relative quantification of phoD and phoX expression levels. Our results confirmed that the distribution of APase is prevalent in cyanobacteria and thus provides a new insight into the potential role of cyanobacterial APase on phosphorus acquisition in natural environment.     

Total and active microbial communities and <Emphasis Type="Italic">phoD</Emphasis> as affected by phosphate depletion and pH in soil

Background and Aims

Soil microbial communities contribute to organic phosphorus cycling in a variety of ways, including secretion of the PhoD alkaline phosphatase. We sampled a long-term grassland fertilization trial in Switzerland characterized by a natural pH gradient. We examined the effects of phosphate depletion and pH on total and active microbial community structures and on the structure and composition of the total and active phoD-harboring community.

Methods

Archaeal, bacterial and fungal communities were investigated using T-RFLP and phoD-harboring members of these communities were identified by 454-sequencing.

Results

Phosphate depletion decreased total, resin-extractable and organic phosphorus and changed the structure of all active microbial communities, and of the total archaeal and phoD-harboring communities. Organic carbon, nitrogen and phosphorus increased with pH, and the structures of all total and active microbial communities except the total fungal community differed between the two pH levels. phoD-harboring members were affiliated to Actinomycetales, Bacilliales, Gloeobacterales, Planctomycetales and Rhizobiales.

Conclusions

Our results suggest that pH and associated soil factors are important determinants of microbial and phoD-harboring community structures. These associated factors include organic carbon and total nitrogen, and to a lesser degree phosphorus status, and active communities are more responsive than total communities. Key players in organic P mineralization are affiliated to phyla that are known to be important in organic matter decomposition.

     

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

An integrated view of bacterial and archaeal diversity in saline soil habitats is essential for understanding the biological and ecological processes and exploiting potential of microbial resources from such environments. This study examined the collective bacterial and archaeal diversity in saline soils using a meta-analysis approach. All available 16S rDNA sequences recovered from saline soils were retrieved from publicly available databases and subjected to phylogenetic and statistical analyses. A total of 9,043 bacterial and 1,039 archaeal sequences, each longer than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on ≥97 % sequence identity), representing 24 known bacterial phyla, with Proteobacteria (44.9 %), Actinobacteria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being predominant. Lysobacter (12.8 %) was the dominant bacterial genus in saline soils, followed by Sphingomonas (4.5 %), Halomonas (2.5 %), and Gemmatimonas (2.5 %). Archaeal sequences were assigned to 602 OTUs, primarily from the phyla Euryarchaeota (88.7 %) and Crenarchaeota (11.3 %). Halorubrum and Thermofilum were the dominant archaeal genera in saline soils. Rarefaction analysis indicated that less than 25 % of bacterial diversity, and approximately 50 % of archaeal diversity, in saline soil habitats has been sampled. This analysis of the global bacterial and archaeal diversity in saline soil habitats can guide future studies to further examine the microbial diversity of saline soils.     

Characterization of Soil Bacterial Communities in Rhizospheric and Nonrhizospheric Soil of Panax ginseng

A culture-independent approach was used to evaluate the bacterial community in rhizospheric and nonrhizospheric soil in which Panax ginseng had grown for 3?years. For each sample, soil was randomly collected from multiple sampling points and mixed thoroughly before genomic DNA extraction. Universal primers 27f and 1492r were used to amplify 16S rRNA genes. Clone libraries were constructed using the amplified 16S rRNA genes, and 192 white clones were chosen for further sequencing. After digestion with restriction endonuclease, 44 operational taxonomic units (OTUs) were generated for rhizospheric and 21 OTUs for nonrhizospheric soils, and the clones of each OTU were sequenced. Blast analysis showed that bacillus, acidobacteria, and proteobacteria were the dominant populations in rhizospheric soil, and proteobacteria were dominant in nonrhizospheric soil. Phylogenetic results showed that bacillus and acidobacteria were clustered into the group of uncultured bacteria in rhizospheric soil; however, proteobacteria were the unique dominant in nonrhizospheric soil.     

Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems

One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems.     

Bacterial Community Diversity in the Brazilian Atlantic Forest Soils

The aim of this study was to characterize the bacterial community diversity of the Brazilian Atlantic forest soil by means of both cultivation and 16S rRNA clone libraries. A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra dos Órgãos (PARNASO), belonged to the genera Arthrobacter, Bacillus, Burkholderia, Leifsonia, Paenibacillus, Pseudomonas, Ralstonia, Serratia, and Streptomyces according to the 16S rRNA sequences. Representative isolates from the different genera degraded cellulose and lignin. The culture-independent analysis based on 894 partial 16S rRNA gene sequences revealed that the most frequently retrieved groups belonged to the phyla Acidobacteria (29–54%), Proteobacteria (16–38%), and Verrucomicrobia (0.6–14%). The majority of the sequences (82.6%) were unidentified singletons and doubletons, indicating a high diversity of rare unique sequences. Chao1 estimator disclosed a high number of phyla (41–152) and species (263–446). This is the first survey on the Atlantic Forest soils using a combination of cultivation and culture-independent approaches. We conclude that the Brazilian Atlantic Forest soil represents a vast source of novel bacteria.     

Effects of nutritional input and diesel contamination on soil enzyme activities and microbial communities in antarctic soils

Pollution of Antarctic soils may be attributable to increased nutritional input and diesel contamination via anthropogenic activities. To investigate the effect of these environmental changes on the Antarctic terrestrial ecosystem, soil enzyme activities and microbial communities in 3 types of Antarctic soils were evaluated. The activities of alkaline phosphomonoesterase and dehydrogenase were dramatically increased, whereas the activities of β-glucosidase, urease, arylsulfatase, and fluorescein diacetate hydrolysis were negligible. Alkaline phosphomonoesterase and dehydrogenase activities in the 3 types of soils increased 3- to 10-fold in response to nutritional input, but did not increase in the presence of diesel contamination. Consistent with the enzymatic activity data, increased copy numbers of the phoA gene, encoding an alkaline phosphomonoesterase, and the 16S rRNA gene were verified using quantitative real-time polymerase chain reaction. Interestingly, dehydrogenase activity and 16S rRNA gene copy number increased slightly after 30 days, even under diesel contamination, probably because of adaptation of the bacterial population. Intact Antarctic soils showed a predominance of Actinobacteria phylum (mostly Pseudonorcarida species) and other phyla such as Proteobacteria, Chloroflexi, Planctomycetes, Firmicutes, and Verrucomicrobia were present in successively lower proportions. Nutrient addition might act as a selective pressure on the bacterial community, resulting in the prevalence of Actinobacteria phylum (mostly Arthrobacter species). Soils contaminated by diesel showed a predominance of Proteobacteria phylum (mostly Phyllobacterium species), and other phyla such as Actinobacteria, Bacteroidetes, Planctomycetes, and Gemmatimonadetes were present in successively lower proportions. Our data reveal that nutritional input has a dramatic impact on bacterial communities in Antarctic soils and that diesel contamination is likely toxic to enzymes in this population.     

Analysis of the Microbial Community Structure by Monitoring an Hg Methylation Gene (hgcA) in Paddy Soils along an Hg Gradient

Knowledge of the diversity of mercury (Hg)-methylating microbes in the environment is limited due to a lack of available molecular biomarkers. Here, we developed novel degenerate PCR primers for a key Hg-methylating gene (hgcA) and amplified successfully the targeted genes from 48 paddy soil samples along an Hg concentration gradient in the Wanshan Hg mining area of China. A significant positive correlation was observed between hgcA gene abundance and methylmercury (MeHg) concentrations, suggesting that microbes containing the genes contribute to Hg methylation in the sampled soils. Canonical correspondence analysis (CCA) showed that the hgcA gene diversity in microbial community structures from paddy soils was high and was influenced by the contents of total Hg, SO₄²⁻, NH₄⁺, and organic matter. Phylogenetic analysis showed that hgcA microbes in the sampled soils likely were related to Deltaproteobacteria, Firmicutes, Chloroflexi, Euryarchaeota, and two unclassified groups. This is a novel report of hgcA diversity in paddy habitats, and results here suggest a link between Hg-methylating microbes and MeHg contamination in situ, which would be useful for monitoring and mediating MeHg synthesis in soils.     

Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils

Background

Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition.

Methodology/Principal Findings

We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found.

Conclusions/Significance

Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland and forest. Furthermore, bacterial community structure was largely driven by tree species and soil pH.     

阿尔泰银莲花根际土壤微生物多样性研究

为了解野生和栽培阿尔泰银莲花根际土壤微生物多样性的差异,该研究采用Illumina MiSeq高通量测序技术对野生和栽培阿尔泰银莲花根际土壤微生物的群落组成和多样性进行探究。结果表明:(1)野生阿尔泰银莲花根际土壤的真菌多样性显著高于栽培阿尔泰银莲花(P<0.05),而细菌多样性差异不显著(P>0.05); NMDS分析结果显示,野生和栽培阿尔泰银莲花根际土壤真菌群落结构差异更显著。(2)细菌9 566个可操作分类单元(OTUs)涉及39门127纲315目500科886属,真菌2 670个OTUs涉及15门57纲138目293科597属。在门水平上,细菌群落中的变形菌门、酸杆菌门、放线菌门及真菌群落中的担子菌门、子囊菌门、被孢霉门均为野生和栽培阿尔泰银莲花根际土壤优势菌门,但其相对丰度在不同生长方式下存在差异。(3)环境因子关联分析(RDA)结果显示,土壤有机质是影响土壤细菌群落的主要因子(P<0.05),土壤pH、碱解氮和有效磷是影响真菌群落的主要因子(P<0.05)。综上认为,野生和栽培下的阿尔泰银莲花根际土壤微生物群落组成和多样性存在显著差异,这种差异可能与不同生长条件下的土壤理化性质存在密切的联系,该研究结果对阿尔泰银莲花科学种植以及土壤改良具有一定意义。     

Bacterial Community Responses to Soils along a Latitudinal and Vegetation Gradient on the Loess Plateau,China

Soil bacterial communities play an important role in nutrient recycling and storage in terrestrial ecosystems. Loess soils are one of the most important soil resources for maintaining the stability of vegetation ecosystems and are mainly distributed in northwest China. Estimating the distributions and affecting factors of soil bacterial communities associated with various types of vegetation will inform our understanding of the effect of vegetation restoration and climate change on these processes. In this study, we collected soil samples from 15 sites from north to south on the Loess Plateau of China that represent different ecosystem types and analyzed the distributions of soil bacterial communities by high-throughput 454 pyrosequencing. The results showed that the 142444 sequences were grouped into 36816 operational taxonomic units (OTUs) based on 97% similarity. The results of the analysis showed that the dominant taxonomic phyla observed in all samples were Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes. Actinobacteria and Proteobacteria were the two most abundant groups in all samples. The relative abundance of Actinobacteria increased from 14.73% to 40.22% as the ecosystem changed from forest to sandy, while the relative abundance of Proteobacteria decreased from 35.35% to 21.40%. Actinobacteria and Proteobacteria had significant correlations with mean annual precipitation (MAP), pH, and soil moisture and nutrients. MAP was significantly correlated with soil chemical and physical properties. The relative abundance of Actinobacteria, Proteobacteria and Planctomycetes correlated significantly with MAP, suggesting that MAP was a key factor that affected the soil bacterial community composition. However, along with the MAP gradient, Chloroflexi, Bacteroidetes and Cyanobacteria had narrow ranges that did not significantly vary with the soil and environmental factors. Overall, we conclude that the edaphic properties and/or vegetation types are driving bacterial community composition. MAP was a key factor that affects the composition of the soil bacteria on the Loess Plateau of China.     

Bacterial Diversity in the Rhizosphere of Cucumbers Grown in Soils Covering a Wide Range of Cucumber Cropping Histories and Environmental Conditions

Rhizosphere microorganisms in soils are important for plant growth. However, the importance of rhizosphere microorganisms is still underestimated since many microorganisms associated with plant roots cannot be cultured and since the microbial diversity in the rhizosphere can be influenced by several factors, such as the cropping history, biogeography, and agricultural practice. Here, we characterized the rhizosphere bacterial diversity of cucumber plants grown in soils covering a wide range of cucumber cropping histories and environmental conditions by using pyrosequencing of bacterial 16S rRNA genes. We also tested the effects of compost addition and/or bacterial inoculation on the bacterial diversity in the rhizosphere. We identified an average of approximately 8,883 reads per sample, corresponding to around 4,993 molecular operational taxonomic units per sample. The Proteobacteria was the most abundant phylum in almost all soils. The abundances of the phyla Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, and Verrucomicrobia varied among the samples, and together with Proteobacteria, these phyla were the six most abundant phyla in almost all analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Flavobacterium, Ohtaekwangia, Opitutus, Gp6, Steroidobacter, and Acidovorax. Overall, compost and microbial amendments increased shoot biomass when compared to untreated soils. However, compost addition decreased the bacterial α-diversity in most soils (but for three soils compost increased diversity), and no statistical effect of microbial amendment on the bacterial α-diversity was found. Moreover, soil amendments did not significantly influence the bacterial β-diversity. Soil organic content appeared more important than compost and microbial amendments in shaping the structure of bacterial communities in the rhizosphere of cucumber.     

Bacterial colonization of a fumigated alkaline saline soil

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m^?1, and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8 %) compared to the unfumigated soil (34.2 %), while that of the Bacteroidetes decreased from 16.2 % in the unfumigated soil to 8.8 % in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7 % in the unfumigated soil to 25.7 %. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.     

Use of a Hierarchical Oligonucleotide Primer Extension Approach for Multiplexed Relative Abundance Analysis of Methanogens in Anaerobic Digestion Systems

In this study, we established a rapid multiplex method to detect the relative abundances of amplified 16S rRNA genes from known cultivatable methanogens at hierarchical specificities in anaerobic digestion systems treating industrial wastewater and sewage sludge. The method was based on the hierarchical oligonucleotide primer extension (HOPE) technique and combined with a set of 27 primers designed to target the total archaeal populations and methanogens from 22 genera within 4 taxonomic orders. After optimization for their specificities and detection sensitivity under the conditions of multiple single-nucleotide primer extension reactions, the HOPE approach was applied to analyze the methanogens in 19 consortium samples from 7 anaerobic treatment systems (i.e., 513 reactions). Among the samples, the methanogen populations detected with order-level primers accounted for >77.2% of the PCR-amplified 16S rRNA genes detected using an Archaea-specific primer. The archaeal communities typically consisted of 2 to 7 known methanogen genera within the Methanobacteriales, Methanomicrobiales, and Methanosarcinales and displayed population dynamic and spatial distributions in anaerobic reactor operations. Principal component analysis of the HOPE data further showed that the methanogen communities could be clustered into 3 distinctive groups, in accordance with the distribution of the Methanosaeta, Methanolinea, and Methanomethylovorans, respectively. This finding suggested that in addition to acetotrophic and hydrogenotrophic methanogens, the methylotrophic methanogens might play a key role in the anaerobic treatment of industrial wastewater. Overall, the results demonstrated that the HOPE approach is a specific, rapid, and multiplexing platform to determine the relative abundances of targeted methanogens in PCR-amplified 16S rRNA gene products.     

Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding

Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m⁻¹ and pH 7.80 (LOW soil), with EC 56 dS m⁻¹ and pH 10.11 (MEDIUM soil) and with EC 159 dS m⁻¹ and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the α- and γ-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.