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Soil Metagenomics

Heng Zhou, Degang Zhang, Zhehao Jiang, Peng Sun, Hailong Xiao, Yuxing Wu, Jiangang Chen
The alpine steppe at Qinghai-Tibetan Plateau is an important area for conserving water source and grassland productivity; however, knowledge about the microbial community structure and function and the risk to human health due to alpine plant-soil ecosystems is limited. Thus, we used prediction methods, such as Tax4Fun, and performed a metagenome pre-study using 16S rRNA sequencing reads for a small scale survey of the microbial communities at degraded alpine steppes (i.e., non-degraded (ND), lightly degraded (LD), moderately degraded (MD), heavily degraded (HD), and extremely degraded (ED) steppes) by Illumina high-throughput sequencing technology...
October 1, 2018: Science of the Total Environment
Gamaliel López-Leal, Fernanda Cornejo-Granados, Juan Manuel Hurtado-Ramírez, Alfredo Mendoza-Vargas, Adrian Ochoa-Leyva
Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by Rhizobiales and Rodobacterales. The analysis of the functions encoded in the metagenome showed enrichment of characteristic features of soil and root-associated bacteria such as ABC-transporters and hydrolase enzymes. Additionally, we found antibiotic resistances genes principally for spectinomycin, tetracycline, and aminoglycosides...
2018: Standards in Genomic Sciences
Gareth Trubl, Ho Bin Jang, Simon Roux, Joanne B Emerson, Natalie Solonenko, Dean R Vik, Lindsey Solden, Jared Ellenbogen, Alexander T Runyon, Benjamin Bolduc, Ben J Woodcroft, Scott R Saleska, Gene W Tyson, Kelly C Wrighton, Matthew B Sullivan, Virginia I Rich
Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i...
September 2018: MSystems
Fei Xia, Jian-Gong Wang, Ting Zhu, Bin Zou, Sung-Keun Rhee, Zhe-Xue Quan
The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB)...
October 12, 2018: Applied and Environmental Microbiology
James Peek, Mirjana Lilic, Daniel Montiel, Aleksandr Milshteyn, Ian Woodworth, John B Biggins, Melinda A Ternei, Paula Y Calle, Michael Danziger, Thulasi Warrier, Kohta Saito, Nathaniel Braffman, Allison Fay, Michael S Glickman, Seth A Darst, Elizabeth A Campbell, Sean F Brady
Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (RifR ). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant RifR mutations...
October 8, 2018: Nature Communications
Min-Jung Kwak, Hyun Gi Kong, Kihyuck Choi, Soon-Kyeong Kwon, Ju Yeon Song, Jidam Lee, Pyeong An Lee, Soo Yeon Choi, Minseok Seo, Hyoung Ju Lee, Eun Joo Jung, Hyein Park, Nazish Roy, Heebal Kim, Myeong Min Lee, Edward M Rubin, Seon-Woo Lee, Jihyun F Kim
Tomato variety Hawaii 7996 is resistant to the soil-borne pathogen Ralstonia solanacearum, whereas the Moneymaker variety is susceptible to the pathogen. To evaluate whether plant-associated microorganisms have a role in disease resistance, we analyzed the rhizosphere microbiomes of both varieties in a mesocosm experiment. Microbiome structures differed between the two cultivars. Transplantation of rhizosphere microbiota from resistant plants suppressed disease symptoms in susceptible plants. Comparative analyses of rhizosphere metagenomes from resistant and susceptible plants enabled the identification and assembly of a flavobacterial genome that was far more abundant in the resistant plant rhizosphere microbiome than in that of the susceptible plant...
October 8, 2018: Nature Biotechnology
Tuan Manh Nguyen, Chan Seo, Moongi Ji, Man-Jeong Paik, Seung-Woon Myung, Jaisoo Kim
Here, a new medium named as intensive soil extract medium (ISEM) based on new soil extract (NSE) using 80% methanol was used to efficiently isolate previously uncultured bacteria and new taxonomic candidates, which accounted for 49% and 55% of the total isolates examined (n=258), respectively. The new isolates were affiliated with seven phyla ( Proteobacteria , Acidobacteria , Firmicutes , Actinobacteria , Verrucomicrobia , Planctomycetes , and Bacteroidetes ). The result of chemical analysis showed that NSE included more diverse components of low-molecular-weight organic substances than two conventional soil extracts made using distilled water...
October 5, 2018: Applied and Environmental Microbiology
Karen G Lloyd, Andrew D Steen, Joshua Ladau, Junqi Yin, Lonnie Crosby
To describe a microbe's physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been studied well, their global abundances, or numbers of cells in any given environment, have not been assessed...
September 2018: MSystems
Roland C Wilhelm, Rahul Singh, Lindsay D Eltis, William W Mohn
Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America...
September 26, 2018: ISME Journal
M H Hemmat-Jou, A A Safari-Sinegani, A Mirzaie-Asl, A Tahmourespour
Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers...
September 21, 2018: Ecotoxicology
Jean-Michel Claverie, Chantal Abergel
Since 1998, when Jim van Etten's team initiated its characterization, Paramecium bursaria Chlorella virus 1 (PBCV-1) had been the largest known DNA virus, both in terms of particle size and genome complexity. In 2003, the Acanthamoeba -infecting Mimivirus unexpectedly superseded PBCV-1, opening the era of giant viruses, i.e., with virions large enough to be visible by light microscopy and genomes encoding more proteins than many bacteria. During the following 15 years, the isolation of many Mimivirus relatives has made Mimiviridae one of the largest and most diverse families of eukaryotic viruses, most of which have been isolated from aquatic environments...
September 18, 2018: Viruses
Paul A Kenward, Rachel L Simister, Connor Morgan-Lang, Niko Finke, Arne Sturm, Steven J Hallam, Sean A Crowe
We developed an efficient, scalable, and inexpensive method for recovering cellular biomass from complex fluid matrices that cannot be processed using conventional filtration methods. The method uses chemical flocculation with iron oxyhydroxides, is capable of recovering >90% of cellular biomass from fluids with more than 103 cells ml-1 , and was validated using both mock communities and field samples. High quality DNA can be readily extracted from iron flocs using standard soil extraction kits. We applied chemical flocculation to fracing fluids from British Columbia, Canada, and recovered a diversity of microbial taxa including abundant members of the Epsilon- and Deltaproteobacteria previously recovered from shale gas operations in the United States...
September 19, 2018: Environmental Microbiology Reports
Marius Bredon, Jessica Dittmer, Cyril Noël, Bouziane Moumen, Didier Bouchon
BACKGROUND: Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action...
September 17, 2018: Microbiome
Ngoc-Loi Nguyen, Woon-Jong Yu, Joo-Han Gwak, So-Jeong Kim, Soo-Je Park, Craig W Herbold, Jong-Geol Kim, Man-Young Jung, Sung-Keun Rhee
Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs ( Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria ), were dominant...
2018: Frontiers in Microbiology
Alexander B Chase, Zulema Gomez-Lunar, Alberto E Lopez, Junhui Li, Steven D Allison, Adam C Martiny, Jennifer B H Martiny
The high diversity of soil bacteria is attributed to the spatial complexity of soil systems, where habitat heterogeneity promotes niche partitioning among bacterial taxa. This premise remains challenging to test, however, as it requires quantifying the traits of closely related soil bacteria and relating these traits to bacterial abundances and geographic distributions. Here, we sought to investigate whether the widespread soil taxon Curtobacterium consists of multiple coexisting ecotypes with differential geographic distributions...
September 13, 2018: Environmental Microbiology
Srinivasa Chaluvadi, Jeffrey L Bennetzen
The rhizosphere microbiome is known to play a crucial role in promoting plant growth, partly by countering soil-borne phytoparasites and by improving nutrient uptake. The abundance and composition of the rhizosphere and root-associated microbiota are influenced by several factors, including plant species and genotype. We hypothesize that crop domestication might influence the composition and diversity of plant-associated microbiomes. We tested the contribution of domestication to the bacterial and archaeal root and soil composition associated with six genotypes of domesticated Setaria italica and four genotypes of its wild ancestor, S...
2018: Frontiers in Plant Science
Sarah E Evans, M Elias Dueker, J Robert Logan, Kathleen C Weathers
Fog supplies water and nutrients to systems ranging from coastal forests to inland deserts. Fog droplets can also contain bacterial and fungal aerosols, but our understanding of fog biology is limited. Using metagenomic tools and culturing, we provide a unique look at fungal and bacterial communities in fog at two fog-dominated sites: coastal Maine (USA) and the Namib Desert (Namibia). Microbial communities in the fog at both sites were diverse, distinct from clear aerosols, and influenced by both soil and marine sources...
January 10, 2019: Science of the Total Environment
Anna Szafranek-Nakonieczna, Agnieszka Wolińska, Urszula Zielenkiewicz, Agnieszka Kowalczyk, Zofia Stępniewska, Mieczysław Błaszczyk
Methanotrophic bacteria are able to use methane (CH4 ) as a sole carbon and energy source. Photochemical oxidation of methane takes place in the stratosphere, whereas in the troposphere, this process is carried out by methanotrophic bacteria. On the one hand, it is known that the efficiency of biological CH4 oxidation is dependent on the mode of land use but, on the other hand, the knowledge of this impact on methanotrophic activity (MTA) is still limited. Thus, the aim of the study was to determine the CH4 oxidation ability of methanotrophic bacteria inhabiting selected arable and no-tillage soils from the Lublin region (Albic Luvisol, Brunic Arenosol, Haplic Chernozem, Calcaric Cambisol) and to identify bacteria involved in this process...
September 1, 2018: Microbial Ecology
Jason C Kimble, Ara S Winter, Michael N Spilde, Robert L Sinsabaugh, Diana E Northup
Low biomass and productivity of arid-land caves with limited availability of nitrogen (N) raises the question of how microbes acquire and cycle this essential element. Caves are ideal environments for investigating microbial functional capabilities, as they lack phototrophic activity and have near constant temperatures and high relative humidity. From the walls of Fort Stanton Cave (FSC), multicolored secondary mineral deposits of soil-like material low in fixed N, known as ferromanganese deposits (FMD), were collected...
November 1, 2018: FEMS Microbiology Ecology
Rachel Mackelprang, Alyssa M Grube, Regina Lamendella, Ederson da C Jesus, Alex Copeland, Chao Liang, Randall D Jackson, Charles W Rice, Stefanie Kapucija, Bayan Parsa, Susannah G Tringe, James M Tiedje, Janet K Jansson
The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis...
2018: Frontiers in Microbiology
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