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Root-knot nematode, Meloidogyne incognita is one of the most important nematodes affecting ginger crop. Rhodopseudomonas palustris PSB-06, as effective microbial fertilizer in increasing plant growth and suppressing soil-borne disease of many crops has been reported. The combination of R. palustris PSB-06 and dazomet treatments had been proved to inhibit root-knot nematode on ginger and increase ginger yield in our preliminary study. The field experiments were conducted to elucidate the reasons behind this finding, and followed by next-generation sequencing to determine the microbial population structures in ginger root rhizosphere. The results showed that combination of R. palustris PSB-06 and dazomet treatment had a synergetic effect by achieving of 80.00% reduction in root-knot nematode numbers less than soil without treatment, and also could increase 37.37% of ginger yield through increasing the contents of chlorophyll and total protein in ginger leaves. Microbiota composition and alpha diversity varied with treatments and growth stages, soil bacterial diversity rapidly increased after planting ginger. In addition, the combined treatment could increase diversity and community composition of probiotic bacteria, and decrease those of soil-borne pathogenic fungi comparing to the soil treated with dazomet alone. Meanwhile, it could also effectively increase soil organic matter, available phosphorus and available potassium. Analysis of correlation between soil microorganisms and physicochemical properties indicated that the soil pH value and available phosphorus content were important factors that could affect soil microorganisms structure at the harvest stage. The bacterial family was more closely correlated with the soil physicochemical properties than the fungal family. Therefore, the combination of R. palustris PSB-06 and dazomet was considered as an effective method to control root-knot nematode disease and improve ginger soil conditions. [ABSTRACT FROM AUTHOR]

Endosulfan, an organochlorine pesticide, has been applied ubiquitously worldwide. However, endosulfan has been identified as a type of persistent organic pollutants (POPs), and its ecotoxicity has drawn attentions from scientists. The present study was implemented to examine the effects of endosulfan on the diversity and structure of soil microorganism communities. A control treatment and three concentrations (0.1, 1.0, and 10.0 mg/kg) were set up in laboratory experiments and sampled on days 7, 14, 21, and 28. The results revealed that the populations of bacteria and actinomycetes decreased significantly after 1.0 and 10.0 mg/kg treatments and that the soil microbial biomass carbon (MBC) was increased by endosulfan compared with the control. Terminal restriction fragment length polymorphism (T-RFLP) results revealed that the soil bacterial diversity was decreased by endosulfan and that the soil microbial community structure became unstable after endosulfan application. Moreover, the results of a 16S rRNA clone library revealed that the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Spirochaetes, and Firmicutes showed an obvious advantage and closely relative. In conclusion, the results of the present study indicated that 0.1-10.0 mg/kg endosulfan showed obvious influences on the diversity and structure of the soil microbial community. [ABSTRACT FROM AUTHOR]

Effects of extremely high carbon dioxide (CO2) concentrations on soil microbial communities and associated processes are largely unknown. We studied a wetland area affected by spots of subcrustal CO2 degassing (mofettes) with focus on anaerobic autotrophic methanogenesis and acetogenesis because the pore gas phase was largely hypoxic. Compared with a reference soil, the mofette was more acidic (ΔpH ∼0.8), strongly enriched in organic carbon (up to 10 times), and exhibited lower prokaryotic diversity. It was dominated by methanogens and subdivision 1 Acidobacteria, which likely thrived under stable hypoxia and acidic pH. Anoxic incubations revealed enhanced formation of acetate and methane (CH4) from hydrogen (H2) and CO2 consistent with elevated CH4 and acetate levels in the mofette soil. 13CO2 mofette soil incubations showed high label incorporations with ∼512 ng 13C g (dry weight (dw)) soil−1 d−1 into the bulk soil and up to 10.7 ng 13C g (dw) soil−1 d−1 into almost all analyzed bacterial lipids. Incorporation of CO2-derived carbon into archaeal lipids was much lower and restricted to the first 10 cm of the soil. DNA-SIP analysis revealed that acidophilic methanogens affiliated with Methanoregulaceae and hitherto unknown acetogens appeared to be involved in the chemolithoautotrophic utilization of 13CO2. Subdivision 1 Acidobacteriaceae assimilated 13CO2 likely via anaplerotic reactions because Acidobacteriaceae are not known to harbor enzymatic pathways for autotrophic CO2 assimilation. We conclude that CO2-induced geochemical changes promoted anaerobic and acidophilic organisms and altered carbon turnover in affected soils. [ABSTRACT FROM AUTHOR]

Despite emergent research initiatives, significant knowledge gaps remain of soil microbiology-associated cadaver decomposition. Nevertheless, preliminary studies have shown that the vast diversity and complex interactions of soil microbial communities have great potential for forensic applications such as clandestine grave location and postmortem interval estimation. This study investigated changes in soil bacterial communities during pig (Sus scrofa domesticus) leg decomposition. 16S rRNA, instead of the usually applied 16S rDNA marker, was used to compare the metabolically active bacteria. Total bacterial RNA was extracted from soil samples of three different layers on day 3,28 and 77 after the shallow burial of a pig leg. The V3 region of the 16S rRNA was amplified, analysed by RT-PCR DGGE, and compared with control soil bacterial community profiles. Statistically significant differences in soil bacterial biodiversity were observed. For the control, bacterial diversity (H0) and species richness (S) of the three layers averaged 2.48 ± 0.14 (H0) and 18.8 ± 2 .5 (S), respectively, while for the test soil increases (p = 0.027) were recorded between day 3 (H0 = 2.71 ±0.02; S = 21.3 ± 2 . 0 ) and 28 (H0 = 3.46±0.32; S = 60.3 ±16.9), particularly in the middle (10-20 cm) and bottom (20-30 cm) soil layers. Between day 28 and 77 the diversity and richness then decreased on average for all three layers (H0 = 3.43 ±0.20; S = 60.0 ±17.3) but remained higher than on day 3. Thus, responses in soil bacterial profiles and activity to carcass decomposition, detected and characterised by RNA-based DGGE, could be used together with RNA sequencing data, changes in physico-chemical variables (carbon, nitrogen, phosphorus, temperature, redox potential, water activity and pH) and conventional macroecology markers (e.g. insects and vegetation), to develop a suite of analytical protocols for different forensic scenarios. [ABSTRACT FROM AUTHOR]

Addition of crystalline cellulose to semi-desert soil shifts the microbial population; this was assessed by following the 16S rRNA gene, glycosyl hydrolase, and measuring its functional diversity in the bacterial population. Quantification of the glycosyl hydrolase gene showed an increase from 1 × 104 g−1 of unamended soil to 3 × 104 g−1 of crystalline-cellulose-amended soil by the 15th day of crystalline cellulose utilization. The indigenous glycosyl hydrolase community in unamended soil was dominated by the clone families that were closely related to the glycosyl hydrolases from Betaproteobacteria and Firmicutes. The addition of crystalline cellulose induced a shift in the glycosyl hydrolase population toward an increase in the relative abundance of the glycosyl hydrolase that was consistent with those of Bacteroidetes and Flavobacteria. The population shift of glycosyl hydrolase was also supported by the comparison of the 16S rRNA gene families in unamended and crystalline-cellulose-amended soil libraries. The most abundant 16S rRNA gene sequences retrieved in the unamended soil were identical to Pseudomonas, Massilia, Paenibacillus, and Bacillus spp., while Cytophaga and Flavobacterium spp. dominated in crystalline-cellulose-amended soil. [ABSTRACT FROM AUTHOR]

Soil habitats contain vast numbers of microorganisms and harbor a large portion of the planet's biological diversity. Although high-throughput sequencing technologies continue to advance our appreciation of this remarkable phylogenetic and functional diversity, we still have only a rudimentary understanding of the forces that allow diverse microbial populations to coexist in soils. This conspicuous knowledge gap may be partially due the human perspective from which we tend to examine soilborne microorganisms. This review focusses on the highly heterogeneous soil matrix from the vantage point of individual bacteria. Methods describing micro-scale soil habitats and their inhabitants based on sieving, dissecting, and visualizing individual soil aggregates are discussed, as are microcosm-based experiments allowing the manipulation of key soil parameters. We identify how the spatial heterogeneity of soil could influence a number of ecological interactions promoting the evolution and maintenance of bacterial diversity. [ABSTRACT FROM AUTHOR]

The relationship between total and metabolically active soil microbial communities can change drastically with environment. In dry lands, water availability is a key factor limiting cells' activity. We surveyed the diversity of total and active Archaea and Bacteria in soils ranging from arid desert to Mediterranean forests. Thirty composited soil samples were retrieved from five sites along a precipitation gradient, collected from patches located between and under the dominant perennial plant at each site. Molecular fingerprinting was used to site-sort the communities according of their 16 S r RNA genes (total community) and their r RNA (active community) amplified by PCR or RT- PCR from directly extracted soil nucleic acids. The differences between soil samples were much higher in total rather than active microbial communities: differences in DNA fingerprints between sites were 1.2 and 2.5 times higher than RNA differences (for Archaea and Bacteria, respectively). Patch-type discrepancies between DNA fingerprints were on average 2.7-19.7 times greater than RNA differences. Moreover, RNA-based community patterns were highly correlated with soil moisture but did not necessarily follow spatial distribution pattern. Our results suggest that in water-limited environments, the spatial patterns obtained by the analysis of active communities are not as robust as those drawn from total communities. [ABSTRACT FROM AUTHOR]

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose (C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N. [ABSTRACT FROM AUTHOR]

Aim This study evaluates the effect of surface application of dried Class A biosolids on microbial populations within copper mine tailings. Methods and Results Mine tailing sites were established at ASARCO Mission Mine close to Sahuarita Arizona. Site 1 ( December 1998) was amended with 248 tons ha−1 of Class A biosolids. Sites 2 ( December 2000) and 3 ( April 2006) were amended with 371 and 270 tons ha−1, respectively. Site D, a neighbouring native desert soil, acted as a control for the evaluation of soil microbial characteristics. Surface amendment of Class A biosolids showed a 4 log10 increase in heterotrophic plate counts (HPCs) compared to unamended tailings, with the increase being maintained for 10-year period. Microbial activities such as nitrification, sulphur oxidation and dehydrogenase activity were also sustained throughout the study period. 16S r RNA clone libraries obtained from community DNA suggest that mine tailings amended with biosolids achieve diversity and bacterial populations similar to native soil bacterial phyla, 10 years postapplication. Conclusion Addition of Class A biosolids to copper mine tailings in the desert south-west increased soil microbial numbers, activity and diversity relative to unamended mine tailings. Significance and Impact of the Study The amended tailings resulted in a functional soil with respect to microbial characteristics, which were sustainable over a 10-year period enabling the development of appropriate vegetation. [ABSTRACT FROM AUTHOR]

Abstract: Bioturbation is known to stimulate microbial communities, especially in macrofaunal burrows where the abundance and activities of bacteria are increased. Until now, these microbial communities have been poorly characterized and an important ecological question remains: do burrow walls harbor similar or specific communities compared with anoxic and surface sediments? The bacterial community structure of coastal sediments inhabited by the polychaete worm Hediste diversicolor was investigated. Surface, burrow wall and anoxic sediments were collected at the Carteau beach (Gulf of Fos, Mediterranean Sea). Bacterial diversity was determined by analyzing small subunit ribosomal RNA (16S rRNA) sequences from three clone libraries (168, 179 and 129 sequences for the surface, burrow wall and anoxic sediments, respectively). Libraries revealed 306 different operational taxonomic units (OTUs) belonging to at least 15 bacterial phyla. Bioinformatic analyses and comparisons between the three clone libraries showed that the burrow walls harbored a specific bacterial community structure which differed from the surface and anoxic environments. More similarities were nevertheless found with the surface assemblage. Inside the burrow walls, the bacterial community was characterized by high biodiversity, which probably results from the biogeochemical heterogeneity of the burrow system. [Copyright &y& Elsevier]

Abstract: Long-term diversity-disturbance responses of soil bacterial communities to copper were determined from field-soils (Spalding; South Australia) exposed to Cu in doses ranging from 0 through to 4012mgCukg−1 soil. Nearly 6 years after application of Cu, the structure of the total bacterial community showed change over the Cu gradient (PCR-DGGE profiling). 16S rRNA clone libraries, generated from unexposed and exposed (1003mgCu addedkg−1 soil) treatments, had significantly different taxa composition. In particular, Acidobacteria were abundant in unexposed soil but were nearly absent from the Cu-exposed sample (P<0.05), which was dominated by Firmicute bacteria (P<0.05). Analysis of community profiles of Acidobacteria, Bacillus, Pseudomonas and Sphingomonas showed significant changes in structural composition with increasing soil Cu. The diversity (Simpsons index) of the Acidobacteria community was more sensitive to increasing concentrations of CaCl-extractable soil Cu (CuExt) than other groups, with decline in diversity occurring at 0.13CuExt mgkg−1 soil. In contrast, diversity in the Bacillus community increased until 10.4CuExt mgkg−1 soil, showing that this group was 2 orders of magnitude more resistant to Cu than Acidobacteria. Sphingomonas was the most resistant to Cu; however, this group along with Pseudomonas represented only a small percentage of total soil bacteria. Changes in bacterial community structure, but not diversity, were concomitant with a decrease in catabolic function (BioLog). Reduction in function followed a dose-response pattern with CuExt levels (R 2=0.86). The EC50 for functional loss was 0.21CuExt mgkg−1 soil, which coincided with loss of Acidobacteria diversity. The microbial responses were confirmed as being due to Cu and not shifts in soil pH (from use of CuSO4) as parallel Zn-based field plots (ZnSO4) were dissimilar. Changes in the diversity of most bacterial groups with soil Cu followed a unimodal response – i.e. diversity initially increased with Cu addition until a critical value was reached, whereupon it sharply decreased. These responses are indicative of the intermediate-disturbance-hypothesis, a macroecological theory that has not been widely tested in environmental microbial ecosystems. [Copyright &y& Elsevier]

Abstract: The effect of copper on the abundance, diversity and resistance of viable heterotrophic and copper resistant bacterial populations (CuR) was evaluated in soils differing only by their amount and type of organic matter. These soils have been obtained using a vineyard soil that had been subjected to three different organic matter managements (Not Amended (NA) or amended with Straw (S) or Conifer Compost (CC)) in a long term field experiment. Soil microcosms were artificially contaminated with copper (250 mg Cu kg−1 of soil) and incubated for 35 days. Throughout the incubation, a differential copper impact on viable heterotrophic and CuR bacterial enumeration was demonstrated according to the soil organic status with a magnitude which followed the order: NA > CC ≥ S. Diversity of CuR bacteria revealed no significant difference between the uncontaminated soils, as determined by 16S rRNA sequencing. However, copper spiking induced an enrichment of particular populations depending on soil, with Methylobacterium, Ralstonia and Staphylococcus like species becoming dominant in NA, S and CC soils, respectively. Evaluation of the copA gene distribution and diversity, through PCR detection and sequencing, revealed that few CuR bacteria (from 7 to 13%) possessed this genetic determinant before the addition of metal. Copper contamination induced an increase in the dissemination of homologous copA genes only in Ralstonia like species indigenous to S soils. From a functional point of view, copper minimum inhibitory concentration for each CuR strain was measured. It did not highlight variable copper resistance efficiency between strains belonging to different taxonomic groups, harboring or not the copA gene, and originating from different soils contaminated or not by copper. [Copyright &y& Elsevier]