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Soil Metagenomics

Chang-Muk Lee, Su-Yeon Kim, Sang-Hong Yoon, Jung-Bong Kim, Yoon-Soo Yeo, Joon-Soo Sim, Bum-Soo Hahn, Dong-Gwan Kim
In an effort to isolate novel natural antibiotics, we searched for antibacterial long-chain N-acyl amino acid synthase (NAS) genes from 70,000 soil metagenome clones by Bacillus subtilis-overlaying screening. In an antibacterial cosmid clone, YS92B, a single gene nasYPL was responsible for the production of the Nas. nasYPL was 903 bp long, and the deduced amino acid sequence showed the highest 71% identity with a hypothetical protein from Massilia niastensis. Phylogenetic analysis demonstrated that NasYPL belongs to Group 1 Nas...
February 13, 2019: Journal of Biotechnology
Getahun E Agga, Kimberly L Cook, Annesly M P Netthisinghe, Rebecca A Gilfillen, Paul B Woosley, Karamat R Sistani
Confined animal feeding operations can facilitate the spread of genes associated with antibiotic resistance. It is not known how cattle removal from beef cattle backgrounding operation affects the persistence of antibiotic resistance genes (ARGs) in the environment. We investigated the effect of cessation of beef cattle backgrounding operation on the persistence and distribution of ARGs in the beef cattle backgrounding environment. The study was conducted at a pasture-feedlot type beef cattle backgrounding operation which consisted of feeding and grazing areas that were separated by a fence with an access gate...
2019: PloS One
Haiyang Chen, Xiaomei Bai, Lijun Jing, Ruihui Chen, Yanguo Teng
The over-use of antibiotics causes growing concerns about human health risks induced by increasing rates of antimicrobial resistance. Riverine systems are considered generally as a natural reservoir of antibiotic resistance genes (ARGs). In this study, several methods including high-throughput sequencing-based metagenomics approach, statistical analysis and network analysis were applied jointly to characterize the wide-spectrum profile of ARGs in the sediments of an urban river in Beijing. Furthermore, contribution of human activities for the presence of ARGs was identified through comparative studies on the metagenomic profiling of ARGs between the river sediments and pristine niches (remote Antarctic soils and deep sea sediments)...
February 25, 2019: Science of the Total Environment
Bela Hausmann, Claus Pelikan, Thomas Rattei, Alexander Loy, Michael Pester
Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize " Candidatus Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling...
February 12, 2019: MBio
Markus Gastauer, Mabel Patricia Ortiz Vera, Kleber Padovani de Souza, Eder Soares Pires, Ronnie Alves, Cecílio Frois Caldeira, Silvio Junio Ramos, Guilherme Oliveira
Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis...
February 12, 2019: Scientific Data
Ruben V Uribe, Eric van der Helm, Maria-Anna Misiakou, Sang-Woo Lee, Stefan Kol, Morten O A Sommer
CRISPR-Cas systems in bacteria and archaea provide immunity against bacteriophages and plasmids. To overcome CRISPR immunity, phages have acquired anti-CRISPR genes that reduce CRISPR-Cas activity. Using a synthetic genetic circuit, we developed a high-throughput approach to discover anti-CRISPR genes from metagenomic libraries based on their functional activity rather than sequence homology or genetic context. We identified 11 DNA fragments from soil, animal, and human metagenomes that circumvent Streptococcus pyogenes Cas9 activity in our selection strain...
January 31, 2019: Cell Host & Microbe
Changsheng Wu, Zhuo Shang, Christophe Lemetre, Melinda A Ternei, Sean F Brady
The growing threat of antibiotic resistance necessitates the discovery of antibiotics that are active against resistant pathogens. Calcium-dependent antibiotics are a small family of structurally diverse acidic lipopeptides assembled by non-ribosomal peptide synthetases (NRPSs) that are known to display various modes of action against antibiotic-resistant pathogens. Here we use NRPS adenylation (AD) domain sequencing to guide the identification, recovery and cloning of the cde biosynthetic gene cluster from a soil metagenome...
February 8, 2019: Journal of the American Chemical Society
Timothy M Ghaly, Jemma L Geoghegan, John Alroy, Michael R Gillings
Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their diversity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils sampled across Australia and Antarctica. We recovered 44,970 open reading frames that encoded 27,215 unique proteins, representing an order of magnitude more cassettes than previous sequencing efforts...
February 6, 2019: Environmental Microbiology
Yanjun Ma, Julie L Zilles, Angela D Kent
Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality, and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups...
February 6, 2019: Environmental Microbiology
Dennis Goss-Souza, Lucas William Mendes, Clovis Daniel Borges, Jorge L M Rodrigues, Siu Mui Tsai
The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due liming and fertilization in long-term no-till cropping...
February 1, 2019: FEMS Microbiology Ecology
Wencong Shi, Mingcong Li, Guangshan Wei, Renmao Tian, Cuiping Li, Bing Wang, Rongshan Lin, Chunyu Shi, Xiuli Chi, Bo Zhou, Zheng Gao
BACKGROUND: Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels...
February 1, 2019: Microbiome
Genis Andrés Castillo Villamizar, Heiko Nacke, Laura Griese, Lydia Tabernero, Katrina Funkner, Rolf Daniel
Protein tyrosine phosphatases (PTPs) fulfil multiple key regulatory functions. Within the group of PTPs, the atypical lipid phosphatases (ALPs) are known for their role as virulence factors associated with human pathogens. Another group of PTPs, which is capable of using inositol-hexakisphosphate (InsP₆) as substrate, are known as phytases. Phytases play major roles in the environmental phosphorus cycle, biotechnology, and pathogenesis. So far, all functionally characterized PTPs, including ALPs and PTP-phytases, have been derived exclusively from isolated microorganisms...
January 29, 2019: Genes
Ho-Kyung Song, Yu Shi, Teng Yang, Haiyan Chu, Jin-Sheng He, Hyoki Kim, Piotr Jablonski, Jonathan M Adams
Studying how metagenome composition and diversity varies along environmental gradients may improve understanding of the general principles of community and ecosystem structuring. We studied soil bacterial metagenomes along a precipitation gradient on the eastern Tibetan Plateau, varying between 500 mm and 60 mm mean annual precipitation (MAP). We found that lower MAP was strongly associated with reduced functional diversity of bacterial genes. It appears that extreme environmental conditions associated with aridity constrain the diversity of functional strategies present in soil biota - analogous to broad scale patterns found in plant functional diversity along environmental gradients...
January 29, 2019: Scientific Reports
Genis Andrés Castillo Villamizar, Heiko Nacke, Marc Boehning, Kristin Herz, Rolf Daniel
Phosphatases, including phytases, play a major role in cell metabolism, phosphorus cycle, biotechnology, and pathogenic processes. Nevertheless, their discovery by functional metagenomics is challenging. Here, soil metagenomic libraries were successfully screened for genes encoding phosphatase activity. In this context, we report the largest number and diversity of phosphatase genes derived from functional metagenome analysis. Two of the detected gene products carry domains which have never been associated with phosphatase activity before...
January 29, 2019: MBio
Alexander Burkert, Thomas A Douglas, Mark P Waldrop, Rachel Mackelprang
Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods such as metagenomic and 16S rRNA gene sequencing. However, these methods do not distinguish between active, dead, and dormant cells. This is of particular concern in ancient permafrost where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy...
January 25, 2019: Applied and Environmental Microbiology
Kathryn M Docherty, Jessica L M Gutknecht
Tractable practices for soil microbial restoration in tallgrass prairies reclaimed from agriculture are a critical gap in traditional ecological restoration. Long-term fertilization and tilling permanently alter soil bacterial and fungal communities, requiring microbe-targeted restoration methods to improve belowground ecosystem services and carbon storage in newly restored prairies. These techniques are particularly important when restoring for climate-ready ecosystems, adapted to altered temperature regimes...
January 25, 2019: Ecological Applications: a Publication of the Ecological Society of America
Chengyue Liang, Yong Huang, Yun Wang, Quanhui Ye, Zuotao Zhang, Hui Wang
PAH ring-hydroxylating dioxygenases (PAH-RHDα) gene, a useful biomarker for PAH-degrading bacteria, has been widely used to examine PAH-degrading bacterial community in different contaminated sites. However, the distribution of PAH-RHDα genes in oilfield soils and mangrove sediments and their relationship with environmental factors still remain largely unclear. In this study, gene-targeted metagenomics was first used to investigate the diversity of PAH-degrading bacterial communities in oilfield soils and mangrove sediments...
January 19, 2019: Applied Microbiology and Biotechnology
Shuo Jiao, Weimin Chen, Gehong Wei
Lacking knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of different plant growth were explored via sequencing of the 16S rRNA amplicon and shotgun metagenomics...
January 18, 2019: Applied and Environmental Microbiology
Balamurugan Sadaiappan, Chinnamani Prasannakumar, Kumaran Subramanian, Mahendran Subramanian
Bacterial diversity studies in hypersaline soil often yield novel organisms and contribute to our understanding of this extreme environment. Soil from Mad Boon is previously uncharacterized, with dense mangrove forest in one side and hypersaline soil in another side of backwater located in Southeast coast of Tamil Nadu, India. We surveyed to characterize the structure and diversity of the bacterial community. Samples were collected in a partially vegetated upland, exposed backwater sedimentation and water-logged location...
February 2019: Data in Brief
Michael BenIsrael, Philipp Wanner, Ramon Aravena, Beth L Parker, Elizabeth A Haack, David T Tsao, Kari E Dunfield
Biodegradation is an important mechanism of action of phytoremediation systems, but performance evaluation is challenging. We applied metagenomic molecular approaches and compound-specific stable carbon isotope analysis to assess biodegradation of toluene in the vadose zone at an urban pilot field system where hybrid poplars were planted to remediate legacy impacts to an underlying shallow fractured bedrock aquifer. Carbon isotope ratios were compared spatio-temporally between toluene dissolved in groundwater and in the vapor phase...
January 16, 2019: International Journal of Phytoremediation
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