Microbial Genetic Diversity Research Articles

Decoupled response of microbial taxa and functions to nutrients: The role of stoichiometry in plantations

The resource quantity and elemental stoichiometry play pivotal roles in shaping belowground biodiversity. However, a significant knowledge gap remains regarding the influence of different plant communities established through monoculture plantations on soil fungi and bacteria's taxonomic and functional dynamics. This study aimed to elucidate the mechanisms underlying the regulation and adaptation of microbial communities at the taxonomic and functional levels in response to communities formed over 34 years through monoculture plantations of coniferous species (Japanese larch, Armand pine, and Chinese pine), deciduous forest species (Katsura), and natural shrubland species (Asian hazel and Liaotung oak) in the temperate climate. The taxonomic and functional classifications of fungi and bacteria were examined for the mineral topsoil (0–10 cm) using MiSeq-sequencing and annotation tools of microorganisms (FAPROTAX and Funguild). Soil bacterial (6.52 ± 0.15) and fungal (4.46 ± 0.12) OTUs' diversity and richness (5.83*103±100 and 1.12*103±46.4, respectively) were higher in the Katsura plantation compared to Armand pine and Chinese pine. This difference was attributed to low soil DOC/OP (24) and DON/OP (11) ratios in the Katsura, indicating that phosphorus availability increased microbial community diversity. The Chinese pine plantation exhibited low functional diversity (3.34 ± 0.04) and richness (45.2 ± 0.41) in bacterial and fungal communities (diversity 3.16 ± 0.15 and richness 56.8 ± 3.13), which could be attributed to the high C/N ratio (25) of litter. These findings suggested that ecological stoichiometry, such as of enzyme, litter C/N, soil DOC/DOP, and DON/DOP ratios, was a sign of the decoupling of soil microorganisms at the genetic and functional levels to land restoration by plantations. It was found that the stoichiometric ratios of plant biomass served as indicators of microbial functions, whereas the stoichiometric ratios of available nutrients in soil regulated microbial genetic diversity. Therefore, nutrient stoichiometry could serve as a strong predictor of microbial diversity and composition during forest restoration.

Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products.

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.

Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach

BackgroundGoat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities.ResultsBacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat’s rumen metagenome are unique with only 56–59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity.ConclusionsIn summary, this study provided the database resources of bacterial metagenomes from goat’s rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.

Komunitas Mikrob pada Hasil Fermentasi Nata De Coco Berdasarkan Marka Random Amplified Polymorphic DNA

Traditional nata de coco fermentation often results in inconsistent nata thickness. From the producer's perspective, thin nata sheets are detrimental because most fermentation media will be wasted. The main cause of this condition may be that the microbial population in the starter culture is different in each batch. It is necessary to observe the cultured microbial community on various qualities of available thick and thin nata to design a better nata de coco starter culture. This study showed thick nata had more Komagataeibacter intermedius bacteria (pellicle forming) than thin nata. In traditional nata fermentation, K. intermedius always coexists with other microbes from the bacteria and yeast groups. Random Amplified Polymorphic DNA (RAPD) analysis indicated that the genetic diversity of bacteria was higher than that of the yeast group.
 
 Keywords: dendrogram of relationship, fermented food, microbial genetic diversity, nata de coco

Long-term effects of restoration on the links between above-and belowground biodiversity in degraded Horqin sandy grassland, Northern China

Long-term ecological restoration plays an important role in the sustainable development of degraded grassland ecosystem. In this study, the levels of species diversity, genetic diversity and soil microbial diversity in restored grassland were measured by vegetation survey, DNA barcoding and soil microbial high-throughput sequencing technology, so as to explore the relationship between above- and belowground biodiversity and its driving factors in Horqin sandy grassland. In this study, the results found that herb are dominated in restoration grassland types. Plant species richness (SR) from post-non-grazing restoration plot (NGR) communities was significantly higher than other restoration communities (10 ± 1.1, p = 0.004). Genetic diversity indices of dominant plant species in chloroplast DNA (cpDNA), were remarkable greater than nuclear DNA (nrDNA) in each recovering sandy grassland plots (amplitude of difference was 44.8%–70.5% in allelic richness (AR), 81.9%–128.1% in expected heterozygosity (HE)). The soil bacterial and fungal richness from natural mobile dune grassland (NM) communities was notably lower than that from recovering grassland types (1641.9 ± 100.4, p < 0.001; 533 ± 16.6, p < 0.001). In this study, heterogeneous levels of genetic variability among different recovering sandy grassland types were detected. Correlation analyses revealed that there were positive correlations between species diversity and genetic diversity (SR & AR: r = 0.56, R2 = 0.31, p < 0.001; SR & HE: r = 0.33, R2 = 0.11, p = 0.045) and a negative correlation between soil microbial diversity and genetic diversity (r = -0.44, R2 = 0.19, p = 0.005). The final structural equation model explained 38% of the variance in SR, 57% in AR, 52% in soil microbial diversity (SD), 49% in aboveground biomass (AGB), 87% in soil organic carbon (SOC), 47% in soil alkali-hydrolyzable nitrogen (SAN) and 69% in soil available phosphorus (SOP). Long-term ecological restoration had significant direct positive effects on AGB, SOC, SAN, SOP, AR, SR and SD. There was a negative correlation between above- and belowground biodiversity and biological and abiotic factors. The results of this study have clarified the above- and underground biodiversity levels of sandy grassland and the relationship with driving factors under long-term ecological restoration measures, and will provide effective support for the management and sustainable development of sandy grassland.

The Microbial Genetic Diversity and Succession Associated with Processing Waters at Different Broiler Processing Stages in an Abattoir in Australia

The high organic content of abattoir-associated process water provides an alternative for low-cost and non-invasive sample collection. This study investigated the association of microbial diversity from an abattoir processing environment with that of chicken meat. Water samples from scalders, defeathering, evisceration, carcass-washer, chillers, and post-chill carcass rinsate were collected from a large-scale abattoir in Australia. DNA was extracted using the Wizard® Genomic DNA Purification Kit, and the 16S rRNA v3-v4 gene region was sequenced using Illumina MiSeq. The results revealed that the Firmicutes decreased from scalding to evisceration (72.55%) and increased with chilling (23.47%), with the Proteobacteria and Bacteroidota changing inversely. A diverse bacterial community with 24 phyla and 392 genera was recovered from the post-chill chicken, with Anoxybacillus (71.84%), Megamonas (4.18%), Gallibacterium (2.14%), Unclassified Lachnospiraceae (1.87%), and Lactobacillus (1.80%) being the abundant genera. The alpha diversity increased from scalding to chilling, while the beta diversity revealed a significant separation of clusters at different processing points (p = 0.01). The alpha- and beta-diversity revealed significant contamination during the defeathering, with a redistribution of the bacteria during the chilling. This study concluded that the genetic diversity during the defeathering is strongly associated with the extent of the post-chill contamination, and may be used to indicate the microbial quality of the chicken meat.

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

Despite extensive efforts to address it, the vastness of uncharacterized ‘dark matter’ microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36–88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.

New Approach for Mining Site Reclamation Using Alternative Substrate Based on Phosphate Industry By-Product and Sludge (Part 2): Metals Transfer to Plant and Soil Microbial Density

The objective of this study was to evaluate the effect of mixtures of the phosphate industry’s by-products and sewage sludge on some heavy metals (Pb, Zn and Cd) in the soil–plant system and the microbial load (bacteria, fungi and actinobacteria) in the soil. The experimental layout was a completely randomized design with ten treatments and four replications. The treatments consist of a combination of five substrates: phosphogypsum (PG), phosphate sludge (PS), sewage sludge (SS), phosphate waste rocks (PWR) and original mine topsoil (TS). Heavy metals analysis, phytoextraction efficiency (PEE) and bioconcentration factor (BCF) were carried out for three Ryegrass cuts. The microbial load of each treatment was determined at the end of the experiment. The results showed that the Pb, Zn and Cd contents of the treatments were well below the permissible limits given in the literature. The highest BCF and PEE were with treatment T4. Furthermore, bacteria, fungi and actinobacteria were significantly influenced by the different proportions of by-products used in the treatments, with the highest richness observed for the T4 treatment. For a successful reclamation of mine sites, it would be useful to determine the speciation of metals in the soil solution and the microbial genetic diversity.

A genome and gene catalog of glacier microbiomes.

Glaciers represent a unique inventory of microbial genetic diversity and a record of evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is particularly vulnerable to global warming. By sequencing 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice and cryoconite habitats, we present a specialized glacier microbial genome and gene catalog to archive glacial genomic and functional diversity. This comprehensive Tibetan Glacier Genome and Gene (TG2G) catalog includes 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes, the utility of which is demonstrated by the exploration of secondary metabolite biosynthetic potentials, virulence factor identification and global glacier metagenome comparison. The TG2G catalog is a valuable resource that enables enhanced understanding of the structure and functions of Tibetan glacial microbiomes.

Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health.

The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-generation sequencing (NGS)-based molecular-biological methods have revealed information on soil biodiversity; however, whether this biodiversity is related to soil health remains unclear. In this study, we performed NGS on grassland surface soil to compare the prokaryotic and eukaryotic genetic diversity to determine the chemical soil quality and examined markers associated with soil health. Microorganisms associated with the nitrogen cycle, bioremediation, plant pathogenicity, antibiotic production, and material degradation showed potential for use as markers. To propose a framework for soil health assessment, we not only used traditional indicators, such as chemical and physical measures, but also assessed metagenomics data of soil by land use to identify the major factors influencing the microbial structure in soil. Moreover, major keystone species were identified. Furthermore, the microbial genetic diversity of generally healthy surface soil, such as forests, farmland, and parks, was determined. These findings provide basic data for exploring soil health-related biomarkers.

Genetic and functional diversity of soil bacteria and fungi from different microhabitats in a karst region in Southern China

Little is known about the difference between bacterial and fungal genetic and functional diversity in karst regions of south China. In this study, the genetic and functional diversity of bacteria and fungi in nine types of soil microenvironments in the karst region in Maolan National Nature Reserve in Guizhou were investigated by PCR-DGGE (Denaturing Gradient Gel Electrophoresis) and BIOLOG EcoPlates. Maolan National Nature Reserve is a UNESCO Biosphere Reserve and plays an important role in protecting the karst forest ecosystem and rare and endangered wild animals and plants in central Asia. The results showed that the diversity of both bacteria and fungi was high and the main factors influencing the diversity of bacteria and fungi were different. The bacterial community structure from different microhabitats under the same vegetation type had higher similarity than similar microhabitats in different vegetation types, which could indicate that the bacterial community structure was mainly controlled by vegetation. For fungi, similar microhabitat species under different vegetation types had higher similarities than different microhabitats species under the same vegetation type, which could indicate that the fungal community structure is mainly controlled by microhabitats. In addition, the metabolic patterns of similar microhabitats in different vegetation were different, while the metabolic patterns of different microhabitats in the same vegetation were not obviously different. In conclusion, the effect of vegetation types on soil microbial functional diversity was greater than that of microhabitats, and this difference was reflected by the different degrees of influence on soil microbial genetic diversity and community structure.

In action-an early warning system for the detection of unexpected or novel pathogens.

Proactive approaches in preventing future epidemics include pathogen discovery prior to their emergence in human and/or animal populations. Playing an important role in pathogen discovery, high-throughput sequencing (HTS) enables the characterization of microbial and viral genetic diversity within a given sample. In particular, metagenomic HTS allows the unbiased taxonomic profiling of sequences; hence, it can identify novel and highly divergent pathogens such as viruses. Newly discovered viral sequences must be further investigated using genomic characterization, molecular and serological screening, and/or invitro and invivo characterization. Several outbreak and surveillance studies apply unbiased generic HTS to characterize the whole genome sequences of suspected pathogens. In contrast, this study aimed to screen for novel and unexpected pathogens in previously generated HTS datasets and use this information as a starting point for the establishment of an early warning system (EWS). As a proof of concept, the EWS was applied to HTS datasets and archived samples from the 2018–9 West Nile virus (WNV) epidemic in Germany. A metagenomics read classifier detected sequences related to genome sequences of various members of Riboviria. We focused the further EWS investigation on viruses belonging to the families Peribunyaviridae and Reoviridae, under suspicion of causing co-infections in WNV-infected birds. Phylogenetic analyses revealed that the reovirus genome sequences clustered with sequences assigned to the species Umatilla virus (UMAV), whereas a new peribunyavirid, tentatively named ‘Hedwig virus’ (HEDV), belonged to a putative novel genus of the family Peribunyaviridae. In follow-up studies, newly developed molecular diagnostic assays detected fourteen UMAV-positive wild birds from different German cities and eight HEDV-positive captive birds from two zoological gardens. UMAV was successfully cultivated in mosquito C6/36 cells inoculated with a blackbird liver. In conclusion, this study demonstrates the power of the applied EWS for the discovery and characterization of unexpected viruses in repurposed sequence datasets, followed by virus screening and cultivation using archived sample material. The EWS enhances the strategies for pathogen recognition before causing sporadic cases and massive outbreaks and proves to be a reliable tool for modern outbreak preparedness.

Effect of round-shaped silver nanoparticles on the genetic and functional diversity of soil microbial community in soil and “soil-plant” systems

Silver and silver nanoparticles (AgNPs) are extensively used as antimicrobial agents in various products and consequently enter the soil ecosystem, in which they accumulate and can have adverse effects on above and belowground organisms. Since the composition of the soil microbiome could have a significant impact on soil fertility, we focused, in this study, on the effect of AgNPs on soil microbial communities. We evaluated the biomass, plant growth-promoting activities, and microbial genetic (taxonomical) and functional diversity in the soil and the “soil-plant” system using chemical, microbiological, and molecular biological methods, especially qPCR, RFLP, and REP-PCR. By compiling the results of the applied assays, we were able to correlate the changes in genetic diversity with the changes in functional diversity and their impact on the composition of soil organic matter. The effect of AgNPs was predominantly dose-dependent, whereas the concentration 100 mg kgdw−1 had the highest effect on all followed parameters. From the taxonomical point of view, AgNPs had the most significant impact on the relative abundance of Bacteroidetes, which increased in a dose-dependent manner, and Firmicutes, which decreased in a dose-dependent manner, and they caused the predominance of Ascomycota among Fungi. These changes in taxonomic diversity result in a significant decrease in the functional diversity of the microbial communities. Especially for the concentration 100 mg kgdw−1, we detected a significant decrease in the ability of the microbial community to utilize simple carbon substrates, determined by Biolog EcoPlates. We detected also a significant alteration in enzyme activity. The activity of enzymes responsible for depolymerization of complex organic matter was in a dose-dependent manner increased, whereas the highest activity reach samples amended with AgNPs at 100 mg kgdw−1. All these changes result in the accumulation of simple organic matter, which could increase osmotic pressure and have severe consequences on soil fertility. In amended soils, we detected alterations of activity of plant growth-promoting bacteria, specifically in the production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylic acid deaminase, and siderophores. All these activities are related to mitigating abiotic stress. The presence of plants in experimental soil had both a mitigating and deepening effect on the toxicity of AgNPs. Both effects probably relate to the influence of AgNPs on the selection of different microbial communities in the soil and the “soil-plant” system.

Next Generation High Throughput Sequencing to Assess Microbial Communities: An Application Based on Water Quality.

Traditional techniques to identify different contaminants (biological or chemical) in the waters are slow, laborious, and can require specialized expertise. Hence, the rapid determination of water quality using more sensitive and reliable metagenomic based approaches attains special importance. Metagenomics deals with the study of genetic material that is recovered from microbial communities present in environmental samples. In traditional techniques cultivation-based methodologieswere used to describe the diversity of microorganisms in environmental samples. It has failed to function as a robust marker because of limited taxonomic and phylogenetic implications. In this backdrop, high-throughput DNA sequencing approaches have proven very powerful in microbial source tracking because of investigating thefull variety of genome-based analysis such as microbial genetic diversity and population structure played by them. Next generation sequencing technologies can reveal a greater proportion of microbial communities that have not been reported earlier by traditional techniques. The present review highlights the shift from traditional techniquesfor the basic study of community composition to next-generation sequencing (NGS) platforms and their potential applications to the biomonitoring of water quality in relation to human health.

Effects of biochar on bacterial genetic diversity in soil contaminated with cadmium

AbstractBiochar has various ecological effects on heavy metal‐contaminated soils. Biochar can be used to passivate the activity of heavy metals and improve environmental conditions for microbial growth. A greenhouse pot experiment was conducted to explore the diversity of microbes in red soil under cadmium (Cd) stress following the application of wheat straw biochar. The contaminant Cd was prepared at 2.5 mg kg‒1 with deionized water to simulate the heavy metal pollution of red soil under natural conditions, and the proportions of wheat straw biochar used were 2.5% and 10%. The complete genetic diversity of red soil bacteria in this study was evaluated using high‐throughput sequencing. The results showed that the bacterial genetic diversity of Cd‐contaminated red soils was restored with biochar treatment, and recovery with 2.5% biochar was significant. Biochar significantly affected the richness of soil bacteria by 6.79%–21.04%. Forty‐three phyla of bacteria, including Proteobacteria, Acidobacteria and Gemmatimonadetes, constituted the bacterial community in the red soils. Further principal component analysis showed that Cd pollution and biochar application collectively affected the bacterial genetic diversity. Hydrogenophaga, Rubrivivax, Haliscomenobacter, Citrobacter, Methylibium and Azospirillum were indicator strains for Cd‐contaminated red soils, while Steroidobacter, Bradyrhizobium, Anaerolinea, Chloronema Dubinina and Gorlenko were key strains for the biochar remediation of Cd contamination. In conclusion, for soil polluted with 2.5 mg kg Cd‒1, the application of 2.5% wheat straw biochar significantly increases soil microbial abundance and genetic diversity and plays an active role in improving the soil micro‐ecosystem.

Metagenomics Framework for the study of Soil Microbial Communities

Metagenomics provides a skylight into the vast world of microbial diversity that is astonishing in its extent. It can lead to extract the enormous information regarding genetic potential of microorganisms to obtain products and processes of biotechnological value. The metagenomics analysis helps in exploring the whole microbiome of a given sample, for example, soil, air and water sample. Soil is considered as a complex environment, which appears to be a major reservoir of microbial genetic diversity with bacterial, archeal, and eukaryotic taxa. Although the characterization of soil microbial communities have been known for decades, there is still a considerable lack of understanding of the mechanism of interaction and metabolism that exist among members of the microbial community and their ecosystem. This taxonomic diversity is mirrored by the diversity of their protein-encoded function, and life history strategies which regulates the soil property or else the productivity. Existing knowledge, concerning the phylogenetic and the functional diversity, community metabolic potential and consequence of evolutional adaption is based largely on partial information gained from the studies performed on microorganism that have been cultivated from soil on a small scale. Importance of metagenome analysis and basic methodologies in view of soil sample for betterment of human welfare without discriminating the nature is enlighten in the article.

Responses of Microbial Community to Di-(2-ethylhcxyl) Phthalate Contamination in Brown Soil.

Di-(2-ethylhcxyl) phthalate (DEHP) is applied as plasticizer, which results in the pollution of environment. In this study, the effects of DEHP on soil microbial functions, structure and genetic diversity were investigated. The concentration of DEHP in the soil were 0, 0.1, 1, 10 and 50 mg/kg, and the experimental period were 28 days. DEHP reduced the quantity, abundance, species dominance and homogeneity of soil microbes during the first 14 days. In addition, microbial utilization efficiency of carbon (carbohydrates, aliphatics, amino acids, metabolites) was impacted after 28 days, though the effects gradually weakened. Based on denaturing gradient gel electrophoresis and clone library analysis, in the presence of DEHP, the dominant microbes in the DEHP-contaminated soil were Sphingomonas and Bacillus, which belonged to the Acidobacteria and Proteobacteriav, respectively. With 0.1 or 1 mg/kg of DEHP, the relative abundances of Acidobacteria were higher, and with 10 or 50 mg/kg of DEHP, the relative abundances of Proteobacteria were higher.

The Strange Case of Prevotella copri: Dr. Jekyll or Mr. Hyde?

This issue of Cell Host & Microbe highlights the opposite faces of Prevotella copri (P.copri). Tett etal. (2019) and Fehlner-Peach etal. (2019) unravel the complexity of gut dwelling P.copri, whereas Rolhion etal. (2019) explore the P.copri dark side with its ability to potentiate Listeria monocytogenes pathogenicity.

The microbial diversity and structure in peat land forest in Indonesia

Soil of tropical forest ecosystem plays very crucial part in controlling the universal carbon cycle. The isolation of microorganisms and their identification are important for understanding their vital role on transformation of organic matter of this ecosystem. Soil storage maximum microbial genetic diversity because of it’s a multilayered environment. No complete methods were discovered yet to cultivate majority of soil microorganisms. A little is known about microbial structure and their essentiality in tropical peat lands compared to most other terrestrial and oceanic habitats. In providing insight to the impacts of land-use of peat land on microbes in Central Kalimantan, Borneo Indonesia, we examined the community structure and diversity of bacteria and fungi in different peat forest soil including: i) natural peat swamp forest (well mixed swamp forest type); ii) disturbed peat soil and iii) mineral soils by using 454 pyrosequencing technology. The results showed that no significant difference was found for diversity and evenness among the sites of fungal community. However, natural peat swamp forest had the highest species richness (Chao1), which was significantly higher than the other two sites (P<0.05 and P<0.05). According to the OTUs analysis four fungi phyla were obtained of which 45 species were classified. The Ascomycota was the most abundant phylum, followed by Basidiomycota, Zygomycota and Glomeromycota. The natural peat swamp forest and disturbed peat soil harbored the maximum number Ascomycota. On the other hand, mineral soil and natural peat soil contained the highest number of Basidiomycota. The top species in natural peat swamp forest included Sugiyamaella paludigena, Polyancora globosa and Ganoderma gibbosum. The mineral soil enriched the abundance of Penicillium herquei, Sugiyamaella paludigena and the disturbed peat soil contained the highest frequency of Polyancora globosa, Gymnopilus lepidotus. According to the PCoA analysis, the community structure of fungus in natural peat soil differed significantly from mineral soil (P=0.04) and disturbed peat soil (P=0.039). No significant difference was found for bacterial species richness (Chao1) among the sites. The diversity of bacteria in disturbed peat soil significantly differed from the other sites (P<0.05 and P<0.05). eleven bacterial phyla and 53 genera were examined. All of the three sites contained the similar abundance of Proteobacteria. The natural peat swamp forest and disturbed peat soil harbored the most abundant Acidobactria. Genera Mycobacterium, Gp1, Gp13, Gp2, Burkholderia, Actinospica, Aciditerrimonas were found in all the sites. Genera Granulibacter, Gp4, Acidisoma, Clostridium_sensu, Clostridium_ XI were only observed in natural peat swamp forest. Genera Rudaea, Rhodopila, Streptomycetes were found only mineral soil. The PCoA analysis showed that the structure of bacteria in natural peat swamp forest significantly differed from the disturbed peat soil (P=0.045). Overall, the bacterial species richness and diversity are more among the sites than of the fungi.
 J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 133-144

Health Assessment of Nickel‐Contaminated Soils Linked to Chemical and Biological Characteristics

Core Ideas Ni‐contaminated soils were evaluated for microbial function and genetic diversity. Soils with >500 mg kg‐1 total Ni had reduced microbial biomass and respiration. Lower microbial diversity in Ni‐contaminated soils was revealed by genetic sequencing. Soil health indicators were influenced by factors in addition to bioavailable Ni. Soils contaminated historically by refinery nickel (Ni) emissions were subjected to laboratory assays evaluating soil health, including microbial function, biomass, and community diversity, based on high‐throughput DNA sequencing. The assays showed that soils with >500 mg kg−1 total Ni had lower microbial biomass and respiration rates as well as reduced microbial diversity and shifts in prevalent phyla compared with most soils with lower Ni. Soil testing for nutrient status suggested additional limitations due to factors other than Ni contamination, including deficiencies of Mn and other essential elements that could possibly explain reduced microbial function even in relatively uncontaminated soils. A greenhouse soybean assay showed greater Ni uptake from soils with the highest total and 0.01 M CaCl2–extractable Ni, with one of the high‐Ni soils (1900 mg kg−1 total Ni) having a level of CaCl2–extractable Ni predicted to reduce soybean growth by >25%. The study revealed that conventional macroscopic measures of soil health were reflected at the microscopic scale by differences in microbial community composition and diversity as evidenced by DNA analysis. Although soil health indicators were affected by high Ni bioavailability, other factors attributable to local differences in fertility status and organic matter content appeared to have strong influences on these indicators.