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Microbial Dark Matter

Ray Chen, Hon Lun Wong, Brendan Paul Burns
Microorganisms in the environment can produce a diverse range of secondary metabolites (SM), which are also known as natural products. Bioactive SMs have been crucial in the development of antibiotics and can also act as useful compounds in the biotechnology industry. These natural products are encoded by an extensive range of biosynthetic gene clusters (BGCs). The developments in omics technologies and bioinformatic tools are contributing to a paradigm shift from traditional culturing and screening methods to bioinformatic tools and genomics to uncover BGCs that were previously unknown or transcriptionally silent...
February 25, 2019: Medicines (Basel, Switzerland)
Ömer K Coskun, Volkan Özen, Scott D Wankel, William D Orsi
The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H2 18 O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments...
February 19, 2019: ISME Journal
Jörn Piel, Jackson Cahn
The diverse microbes that produce natural products represent an important source of novel therapeutics, drug leads, and scientific tools. However, the vast majority have not been grown in axenic culture and are members of complex communities. While meta-'omic methods such as metagenomics, -transcriptomics, and -proteomics reveal collective molecular features of "microbial dark matter", the study of individual microbiome members can be challenging. To address these limits, a number of techniques with single-bacterial resolution have been developed in the last decade-and-a-half...
February 12, 2019: Angewandte Chemie
Yong-Rong Bian, Bao-Hua Gu, Bo Zhu, Hu Cheng, Cheng-Gang Gu, Xing-Lun Yang, Yang Song, Fang Wang, Mao Ye, Xin Jiang
In sediments, wetlands, and flooded paddy soils, natural organic matter (DOM), such as humic acid (HA) and fulvic acid (FA), exist in a reduced state and mediate the reduction of Hg(Ⅱ) and affect the transformation of mercury and geochemical cycles. This study simulated a dark anaerobic environment to study the reduction of Hg(Ⅱ) by reduced HA and FA. Compared to oxidized HA and FA, the reduction capacity of the reduced HA and FA for Hg(Ⅱ) were higher. The optimal concentrations of reduced HA and FA to reduce Hg(Ⅱ) to Hg(0) were 0...
November 8, 2018: Huan Jing Ke Xue= Huanjing Kexue
Da-Shuai Mu, Qi-Yun Liang, Xiao-Man Wang, De-Chen Lu, Ming-Jing Shi, Guan-Jun Chen, Zong-Jun Du
BACKGROUND: The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be "culturable" may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state...
December 26, 2018: Microbiome
M S Sankar, Padmanava Dash, Shatrughan Singh, YueHan Lu, Andrew E Mercer, Shuo Chen
The objective of this research was to quantify the temporal variation of dissolved organic matter (DOM) in five distinct waterbodies in watersheds with diverse types of land use and land cover in the presence and absence of sunlight. The water bodies were an agricultural pond, a lake in a forested watershed, a man-made reservoir, an estuary, and a bay. Two sets of samples were prepared by dispensing unfiltered samples into filtered samples in 1:10 ratio (V/V). The first set was exposed to sunlight (10 hr per day for 30 days) for examining the combined effect of photo-biodegradation, while the second set was stored in dark for examining biodegradation alone...
March 2019: Journal of Environmental Sciences (China)
Olga V Golyshina, Rafael Bargiela, Peter N Golyshin
Recently, the order Thermoplasmatales was expanded through the cultivation and description of species Cuniculiplasma divulgatum and corresponding family Cuniculiplasmataceae. Initially isolated from acidic streamers, signatures of these archaea were ubiquitously found in various low-pH settings. Eight genomes with various levels of completeness are currently available, all of which exhibit very high sequence identities and genomic conservation. Co-existence of Cuniculiplasmataceae with archaeal Richmond Mine acidophilic nanoorganisms ('ARMAN')-related archaea representing an intriguing group within the "microbial dark matter" suggests their common fundamental environmental strategy and metabolic networking...
November 29, 2018: Extremophiles: Life Under Extreme Conditions
Osnat Tirosh, Sean Conlan, Clay Deming, Shih-Queen Lee-Lin, Xin Huang, Helen C Su, Alexandra F Freeman, Julia A Segre, Heidi H Kong
Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation1-3 , mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial-host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections4 ...
December 2018: Nature Medicine
Janko Tackmann, Natasha Arora, Thomas Sebastian Benedikt Schmidt, João Frederico Matias Rodrigues, Christian von Mering
BACKGROUND: The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers...
October 24, 2018: Microbiome
Christian Rinke
Single-cell genomics allows bypassing the culturing step and to directly access environmental microbes one cell at a time. The method has been successfully applied to explore archaeal and bacterial candidate phyla, referred to as microbial dark matter. Here I summarize the single-cell genomics workflow, including sample preparation and preservation, high-throughput fluorescence-activated cell sorting, cell lysis and amplification of environmental samples. Furthermore I describe phylogenetic screening based on 16S rRNA genes and suggest a suitable library preparation and sequencing approach...
2018: Methods in Molecular Biology
B Y Loulou Peisl, Emma L Schymanski, Paul Wilmes
The "dark matter" in metabolomics (unknowns) represents an exciting frontier with significant potential for discovery in relation to biochemistry, yet it also presents one of the largest challenges to overcome. This focussed review takes a close look at the current state-of-the-art and future challenges in tackling the unknowns with specific focus on the human gut microbiome and host-microbe interactions. Metabolomics, like metabolism itself, is a very dynamic discipline, with many workflows and methods under development, both in terms of chemical analysis and post-analysis data processing...
December 11, 2018: Analytica Chimica Acta
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
Anja Grohmann, Yevhen Vainshtein, Ellen Euchner, Christian Grumaz, Dieter Bryniok, Ralf Rabus, Kai Sohn
Background: Biogas production is an attractive technology for a sustainable generation of renewable energy. Although the microbial community is fundamental for such production, the process control is still limited to technological and chemical parameters. Currently, most of the efforts on microbial management system (MiMaS) are focused on process-specific marker species and community dynamics, but a practical implementation is in its infancy. The high number of unknown and uncharacterized microorganisms in general is one of the reasons hindering further advancements...
2018: Biotechnology for Biofuels
Magdalena Calusinska, Xavier Goux, Marie Fossépré, Emilie E L Muller, Paul Wilmes, Philippe Delfosse
Background: Anaerobic digestion (AD) is a microbe-driven process of biomass decomposition to CH4 and CO2 . In addition to renewable and cost-effective energy production, AD has emerged in the European Union as an environmentally friendly model of bio-waste valorisation and nutrient recycling. Nevertheless, due to the high diversity of uncharacterised microbes, a typical AD microbiome is still considered as "dark matter". Results: Using the high-throughput sequencing of small rRNA gene, and a monthly monitoring of the physicochemical parameters for 20 different mesophilic full-scale bioreactors over 1 year, we generated a detailed view of AD microbial ecology towards a better understanding of factors that influence and shape these communities...
2018: Biotechnology for Biofuels
Julie Callanan, Stephen R Stockdale, Andrey Shkoporov, Lorraine A Draper, R Paul Ross, Colin Hill
The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the "viral dark matter"). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities...
July 21, 2018: Viruses
Amelia Fitch, Chloe Orland, David Willer, Erik J S Emilson, Andrew J Tanentzap
Boreal lakes are major components of the global carbon cycle, partly because of sediment-bound heterotrophic microorganisms that decompose within-lake and terrestrially derived organic matter (t-OM). The ability for sediment bacteria to break down and alter t-OM may depend on environmental characteristics and community composition. However, the connection between these two potential drivers of decomposition is poorly understood. We tested how bacterial activity changed along experimental gradients in the quality and quantity of t-OM inputs into littoral sediments of two small boreal lakes, a dark and a clear lake, and measured the abundance of operational taxonomic units and functional genes to identify mechanisms underlying bacterial responses...
November 2018: Global Change Biology
Ömer K Coskun, Monica Pichler, Sergio Vargas, Stuart Gilder, William D Orsi
Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [13 C]bicarbonate, DNA-qSIP showed that ammonia-oxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter...
September 15, 2018: Applied and Environmental Microbiology
Alexey Vorobev, Shalabh Sharma, Mengyun Yu, Juhyung Lee, Benjamin J Washington, William B Whitman, Ford Ballantyne, Patricia M Medeiros, Mary Ann Moran
Understanding which compounds comprising the complex and dynamic marine dissolved organic matter (DOM) pool are important in supporting heterotrophic bacterial production remains a major challenge. We eliminated sources of labile phytoplankton products, advected terrestrial material and photodegradation products to coastal microbial communities by enclosing water samples in situ for 24 h in the dark. Bacterial genes for which expression decreased between the beginning and end of the incubation and chemical formulae that were depleted over this same time frame were used as indicators of bioavailable compounds, an approach that avoids augmenting or modifying the natural DOM pool...
July 2, 2018: Environmental Microbiology
William D Orsi
Vast regions of the dark ocean have ultra-slow rates of organic matter sedimentation, and their sediments are oxygenated to great depths yet have low levels of organic matter and cells. Primary production in the oxic seabed is supported by ammonia-oxidizing archaea, whereas in anoxic sediments, novel, uncultivated groups have the potential to produce H2 and CH4 , which fuel anaerobic carbon fixation. Subseafloor bacteria have very low mutation rates, and their evolution is likely dominated by selection of different pre-adapted subseafloor taxa under oxic and anoxic conditions...
July 2, 2018: Nature Reviews. Microbiology
Geert Rb Huys, Jeroen Raes
With the vast majority of the microbial world still considered unculturable or undiscovered, microbiologists not only require more fundamental insights concerning microbial growth requirements but also need to implement miniaturized, versatile and high-throughput technologies to upscale current microbial isolation strategies. In this respect, single-cell-based approaches are increasingly finding their way to the microbiology lab. A number of recent studies have demonstrated that analysis and separation of free microbial cells by flow-based sorting as well as physical stochastic confinement of individual cells in microenvironment compartments can facilitate the isolation of previously uncultured species and the discovery of novel microbial taxa...
June 13, 2018: Current Opinion in Microbiology
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