The succession of GH6 cellulase-producing microbial communities and temporal profile of GH6 gene abundance during vermicomposting of maize stover and cow dung

ABSTRACTThis study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance ofAcidobacteriaand theSyntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance ofArchaea(primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by theMethanosarcinalesin the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at MEF, and microbial communities are structured by the dominant shrub,Chamaedaphne calyculata, which may act as a carbon source for major consumers in the peatland.

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The non-negligibility of greenhouse gas emission from a combined pre-composting and vermicomposting system with maize stover and cow dung

Environmental Science and Pollution Research ◽

10.1007/s11356-020-12172-2 ◽

2021 ◽

Author(s):

Lei Zhang ◽

Tingting Zhao ◽

Enhui Shi ◽

Zunhao Zhang ◽

Yan Zhang ◽

...

Keyword(s):

Greenhouse Gas ◽

Greenhouse Gas Emission ◽

Cow Dung ◽

Gas Emission ◽

Maize Stover

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Quantifying functional gene populations: comparing gene abundance and corresponding enzymatic activity using denitrification and nitrogen fixation in pulp and paper mill effluent treatment systems

Canadian Journal of Microbiology ◽

10.1139/w01-092 ◽

2001 ◽

Vol 47 (10) ◽

pp. 925-934 ◽

Cited By ~ 8

Author(s):

Josh D Neufeld ◽

Brian T Driscoll ◽

Roger Knowles ◽

Frederick S Archibald

Keyword(s):

Nitrogen Fixation ◽

Activated Sludge ◽

Microbial Communities ◽

Sequence Similarity ◽

Reaction Rates ◽

Effluent Treatment ◽

Specific Gene ◽

Biochemical Activity ◽

Paper Mill Effluent ◽

Gene Abundance

The relationship between the abundance of three functional genes and their corresponding biochemical reaction rates was investigated in several activated sludge and mill effluent microbial communities. Gene probes were prepared for two key denitrification genes (nirS and nirK) and for one nitrogen-fixation gene (nifH) and were validated using a variety of strains of known nir and nif genotype. ATP-based measures of viable cell numbers were used to provide total population sizes. In certain microbial communities (activated sludge enrichment cultures and multiple samples taken from the same mill primary clarifier), a strong correlation was observed between gene abundance and biochemical activity rates. However, when comparing several different nonenriched activated sludge bioreactors and separate primary clarifier microbial communities, the ratio of specific gene abundance to biochemical activity rates varied widely. These results suggest that in cases where a microbial community is not fully induced for a given biochemical activity or when very different communities are compared, quantitative gene probing can give a better measure of a community's potential to carry out the encoded function than can the relevant biochemical assay. However, the gene quantitation method employed here probably underestimated the true number of probed genes present in the microbial communities due to nirS and nifH genes in the communities having reduced DNA sequence similarity with the probes used.Key words: denitrification, nitrogen fixation, quantitative hybridization, activated sludge, primary clarifier.

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A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

Biochemical Society Transactions ◽

10.1042/bst20190172 ◽

2020 ◽

Vol 48 (2) ◽

pp. 399-409

Author(s):

Baizhen Gao ◽

Rushant Sabnis ◽

Tommaso Costantini ◽

Robert Jinkerson ◽

Qing Sun

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Environmental Remediation ◽

Real Life ◽

Design Principles ◽

Microbial Interactions ◽

Potential Applications ◽

New Gene ◽

Global Biogeochemical Cycles ◽

Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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T-RFLP – a representative tool to study pulmonary microbial communities

Pneumologie ◽

10.1055/s-0029-1214114 ◽

2009 ◽

Vol 63 (S 01) ◽

Author(s):

T Zakharkina ◽

C Herr ◽

A Yildirim ◽

M Friedrich ◽

R Bals

Keyword(s):

Microbial Communities

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Screening bioactive secondary metabolites from Costa Rican enviromental microbial communities

Planta Medica ◽

10.1055/s-0035-1556400 ◽

2015 ◽

Vol 81 (11) ◽

Author(s):

JJ Araya ◽

M Chavarría ◽

A Pinto-Tomás ◽

C Murillo ◽

L Uribe ◽

...

Keyword(s):

Secondary Metabolites ◽

Microbial Communities ◽

Costa Rican ◽

Bioactive Secondary Metabolites

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Generation and analysis of biogas from kitchen waste at a small scale

WEENTECH Proceedings in Energy ◽

10.32438/wpe.0602134 ◽

2020 ◽

pp. 140-148

Author(s):

Md. Kumail Naqvi ◽

Mrinal Anthwal ◽

Ravindra Kumar

Keyword(s):

Food Waste ◽

Total Solid ◽

Small Scale ◽

Cow Dung ◽

Retention Period ◽

Household Level ◽

Replacement Model ◽

The Everyday ◽

Scale Experiment ◽

Small Period

Biogas is the product of anaerobic vitiation of biodegradable matter. This paper focuses on the need of alternative and green sources of energy at a household level and how biogas produced from the everyday organic waste has the potential and possibility to replace LPG cylinders at houses, shops etc. and empower us to step towards an eco-friendly future. The purpose this small-scale experiment has been to find the perfect input matter that is easy to acquire and which produces the maximum amount of gas from minimum input and within small period of waste retention. Four different types of input waste material containing different quantities of cow dung and kitchen food waste were studied through individual experimental setups. Waste was mixed and kept at room temperature and the pH and total solid concentration of the samples were recorded on regular intervals. From the experiment it was found that the optimum yield of biogas at a small scale, based on the parameters such as retention period, pH and total solid con-centration can be obtained by the use of food waste form households and kitchens. The exact composition has been discussed in this paper. The energy generated by the small-scale generator has also been compared to that of an LPG cylinder and an LPG replacement model has also been presented.

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