Molecular analyses of the diversity and function of the family 1 β-glucosidase-producing microbial community in compost

2021 ◽  
Author(s):  
Xinyue Zhang ◽  
Erlie Su ◽  
Shanshan Li ◽  
Xiehui Chen ◽  
Zhihua Fan ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Environmental Changes ◽  
Diversity Index ◽  
Cellulose Degradation ◽  
Principal Component ◽  
Dna And Rna ◽  
Functional Community ◽  
Genes Encoding ◽  
The Individual ◽  
And Function

The diversity and transcription efficiency of GH1 family β-glucosidase genes were investigated in natural and inoculated composts using a DNA clone library and real-time qPCR. Compositional differences were observed in the functional community between both composting processes. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla. Twenty representative β-glucosidase genes were quantitatively analyzed from DNA and RNA pools. Principal component analysis and Pearson’s correlation analysis showed that cellulose degradation is correlated with the composition and succession of functional microbial communities, and this correlation was mainly observed in Proteobacteria and Actinobacteria. Compared with inoculated compost, the functional microbial communities in natural compost with a low diversity index exhibited weak buffering capacity for function in response to environmental changes. This may explain the consistency and dysfunction of cellulose degradation and transcriptional regulation by dominant β-glucosidase genes. Except for the β-glucosidase genes encoding constitutive enzymes, individual β-glucosidase genes responded to environmental changes more drastically than the group β-glucosidase genes. Correlation results suggested that β-glucosidase genes belonging to Micrococcales played an important role in the regulation of intracellular β-glucosidase. These results indicated that the responses of functional microorganisms were different during both composting processes, and were reflected at both the individual and group levels.

scholarly journals β-Glucosidase genes differentially expressed during composting

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Xinyue Zhang ◽  
Bo Ma ◽  
Jiawen Liu ◽  
Xiehui Chen ◽  
Shanshan Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Environmental Changes ◽  
Cellulose Degradation ◽  
Degradation Mechanism ◽  
Degradation Process ◽  
Global Scale ◽  
Expression Of Genes ◽  
Glucose Tolerant ◽  
Cooling Phase ◽  
And Function

Abstract Background Cellulose degradation by cellulase is brought about by complex communities of interacting microorganisms, which significantly contribute to the cycling of carbon on a global scale. β-Glucosidase (BGL) is the rate-limiting enzyme in the cellulose degradation process. Thus, analyzing the expression of genes involved in cellulose degradation and regulation of BGL gene expression during composting will improve the understanding of the cellulose degradation mechanism. Based on our previous research, we hypothesized that BGL-producing microbial communities differentially regulate the expression of glucose-tolerant BGL and non-glucose-tolerant BGL to adapt to the changes in cellulose degradation conditions. Results To confirm this hypothesis, the structure and function of functional microbial communities involved in cellulose degradation were investigated by metatranscriptomics and a DNA library search of the GH1 family of BGLs involved in natural and inoculated composting. Under normal conditions, the group of non-glucose-tolerant BGL genes exhibited higher sensitivity to regulation than the glucose-tolerant BGL genes, which was suppressed during the composting process. Compared with the expression of endoglucanase and exoglucanase, the functional microbial communities exhibited a different transcriptional regulation of BGL genes during the cooling phase of natural composting. BGL-producing microbial communities upregulated the expression of glucose-tolerant BGL under carbon catabolite repression due to the increased glucose concentration, whereas the expression of non-glucose-tolerant BGL was suppressed. Conclusion Our results support the hypothesis that the functional microbial communities use multiple strategies of varying effectiveness to regulate the expression of BGL genes to facilitate adaptation to environmental changes.

scholarly journals Coral-associated viral communities show high levels of diversity and host auxiliary functions

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4054 ◽  
Author(s):  
Karen D. Weynberg ◽  
Patrick W. Laffy ◽  
Elisha M. Wood-Charlson ◽  
Dmitrij Turaev ◽  
Thomas Rattei ◽  
...  
Keyword(s):  
Coral Species ◽  
Marine Invertebrates ◽  
Dna Viruses ◽  
Dna And Rna ◽  
Ssrna Virus ◽  
Genes Encoding ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
D1 And D2 Proteins ◽  
Green Fluorescent ◽  
And Function

Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent. Most sequences with matches to eukaryotic viruses were assigned to six viral families, including four Nucleocytoplasmic Large DNA Viruses (NCLDVs) families: Iridoviridae, Phycodnaviridae, Mimiviridae, and Poxviridae, as well as Retroviridae and Polydnaviridae. Contrary to previous findings, Herpesvirales were rare in these GBR corals. Sequences of a ssRNA virus with similarities to the dinornavirus, Heterocapsa circularisquama ssRNA virus of the Alvernaviridae that infects free-living dinoflagellates, were observed in three coral species. We also detected viruses previously undescribed from the coral holobiont, including a virus that targets fungi associated with the coral species Acropora tenuis. Functional analysis of the assembled contigs indicated a high prevalence of latency-associated genes in the coral-associated viral assemblages, several host-derived auxiliary metabolic genes (AMGs) for photosynthesis (psbA, psbD genes encoding the photosystem II D1 and D2 proteins respectively), as well as potential nematocyst toxins and antioxidants (genes encoding green fluorescent-like chromoprotein). This study expands the currently limited knowledge on coral-associated viruses by characterising viral composition and function across seven GBR coral species.

Clearer than mud? Using environmental DNA to track historical shifts in lake communities.

2021 ◽  
Author(s):  
John Pearman ◽  
Laura Biessy ◽  
Georgia Thomson-Laing ◽  
Lizette Reyes ◽  
Claire Shepherd ◽  
...  
Keyword(s):  
New Zealand ◽  
Microbial Communities ◽  
Environmental History ◽  
Environmental Changes ◽  
Environmental Dna ◽  
Taxonomic Composition ◽  
Molecular Methods ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Dna And Rna

<p>A continuous record of environmental history is stored in lake sediments providing an avenue to explore current and historical lake communities. Traditionally paleolimnological methods have focussed on macroscopic indicators (e.g. pollen, chronomids, diatoms) to investigate environmental changes but the application of environmental DNA techniques has enabled the investigation of microbial communities and other soft bodied organisms through time. The ‘Our lakes’ health; past, present, future (Lakes380)’ project aims to combined traditional and molecular methods to explore shifts in biological communities over the last 1,000 years (pre-human arrival in New Zealand). Sediments cores have been collected from a wide diversity of lakes across New Zealand and 16S rRNA gene metabarcoding approaches of both DNA and RNA applied to reveal how microbial community changes across time and especially in response to the arrival of humans and associated changes to the landscape and lake environments. We further investigate the changes in inferred metabolic potential of the microbial communities as the taxonomic composition of the lake differs over time. Finally, we combine these novel molecular methods with hyperspectral scanning and pollen data to increase the knowledge of changes in lake communities and identifying the timing of changes in lake health. The combination of methodologies provides a greater understanding of the environmental history of lake systems and will help to inform management decisions relating to the restoration and protection of lake health.</p>

scholarly journals Structure and function of three novel MHC class I antigens derived from a C3H ultraviolet-induced fibrosarcoma.

1986 ◽  
Vol 164 (3) ◽  
pp. 794-813 ◽  
Author(s):  
R Linsk ◽  
J Vogel ◽  
H Stauss ◽  
J Forman ◽  
R S Goodenow
Keyword(s):  
Mhc Class I ◽  
Dna Sequence ◽  
Class I ◽  
Gene Encoding ◽  
Functional Conservation ◽  
Mhc Class I Antigens ◽  
Genes Encoding ◽  
Polymorphic Restriction ◽  
The Individual ◽  
And Function

The UV-induced, C3H fibrosarcoma, 1591, expresses at least three unique MHC class I antigens not found on normal C3H tissue. Here we report the complete DNA sequence of the three novel class I genes encoding these molecules, and describe in detail the recognition of the individual products by tumor-reactive and allospecific CTL. Remarkably, although C3H does not appear to express H-2L locus information, this C3H tumor expresses two distinct antigens, termed A149 and A166, which are extremely homologous to each other and to the H-2Ld antigen from BALB/c. The gene encoding the third novel class I antigen from 1591, A216, is quite homologous to H-2Kk) throughout its 3' end. Since all three of these genes account for polymorphic restriction fragments not found in C3H, it is likely that they were derived by recombination from the endogenous class I genes of C3H. The DNA sequence homology of A149, A166, and H-2Ld is especially significant given the functional conservation observed between the products of these genes. Limited sequence substitutions appear to correlate with some of the discrete serological differences observed between these molecules. In addition, both A149 and A166 crossreact, but to differing extents, with H-2Ld at the level of T cell recognition. Our results are consistent with the view that CTL recognize complex conformational determinants on class I molecules, but extend previous observations by comparing a set of antigens with discrete and overlapping structural and functional differences.

scholarly journals Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites

2020 ◽  
Author(s):  
Martyna Marynowska ◽  
Xavier Goux ◽  
David Sillam-Dusses ◽  
Corinne Rouland-Lefevre ◽  
Rashi Halder ◽  
...  
Keyword(s):  
De Novo ◽  
Plant Biomass ◽  
Principal Component ◽  
Valuable Insight ◽  
Functional Characterisation ◽  
Plant Fibre ◽  
Termite Gut ◽  
Genes Encoding ◽  
Scientific Attention ◽  
And Function

Abstract Background: Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humification. Lignocellulose is often a principal component of such plant diet and termites largely rely on their symbiotic microbiota and associated enzymes to decompose their food efficiently. While lower termites and their gut flagellates were given larger scientific attention in the past, the gut lignocellulolytic bacteria of higher termites remain less explored. Therefore, in this study, we investigated the structure and function of gut prokaryotic microbiomes from 11 higher termite genera representative of Syntermitinae, Apicotermitinae, Termitidae and Nasutitermitinae subfamilies, broadly grouped into plant fibre- and soil-feeding termite categories. Results: Despite the different compositional structures of the studied termite gut microbiomes, reflecting well the diet and host lineage, we observed a surprisingly high functional congruency between gut metatranscriptomes from both feeding groups. The abundance of transcripts encoding for carbohydrate active enzymes as well as expression and diversity profiles of assigned glycoside hydrolase families were also similar between plant fibre- and soil-feeding termites. Yet, dietary imprints highlighted subtle metabolic differences specific to each feeding category. Roughly 0.18 % of de novo re-constructed gene transcripts were shared between the different termite gut microbiomes, making each termite gut a unique reservoir of genes encoding for potentially industrially applicable enzymes, e.g. relevant to biomass degradation. Taken together, we demonstrated the functional equivalence in microbial populations across different termite hosts.Conclusions: Our results provide valuable insight into the bacterial component of the termite gut system and significantly expand the inventory of termite prokaryotic genes participating in the deconstruction of plant biomass.

scholarly journals Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites

2020 ◽  
Author(s):  
Martyna Marynowska ◽  
Xavier Goux ◽  
David Sillam-Dusses ◽  
Corinne Rouland-Lefevre ◽  
Rashi Halder ◽  
...  
Keyword(s):  
De Novo ◽  
Plant Biomass ◽  
Principal Component ◽  
Valuable Insight ◽  
Functional Characterisation ◽  
Plant Fibre ◽  
Termite Gut ◽  
Genes Encoding ◽  
Scientific Attention ◽  
And Function

Abstract Background: Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humification. Lignocellulose is often a principal component of such plant diet and termites largely rely on their symbiotic microbiota and associated enzymes to decompose their food efficiently. While lower termites and their gut flagellates were given larger scientific attention in the past, the gut lignocellulolytic bacteria of higher termites remain less explored. Therefore, in this study, we investigated the structure and function of gut prokaryotic microbiomes from 11 higher termite genera representative of Syntermitinae, Apicotermitinae, Termitidae and Nasutitermitinae subfamilies, broadly grouped into plant fibre- and soil-feeding termite categories. Results: Despite the different compositional structures of the studied termite gut microbiomes, reflecting well the diet and host lineage, we observed a surprisingly high functional congruency between gut metatranscriptomes from both feeding groups. The abundance of transcripts encoding for carbohydrate active enzymes as well as expression and diversity profiles of assigned glycoside hydrolase families were also similar between plant fibre- and soil-feeding termites. Yet, dietary imprints highlighted subtle metabolic differences specific to each feeding category. Roughly 0.18 % of de novo re-constructed gene transcripts were shared between the different termite gut microbiomes, making each termite gut a unique reservoir of genes encoding for potentially industrially applicable enzymes, e.g. relevant to biomass degradation. Taken together, we demonstrated the functional equivalence in microbial populations across different termite hosts. Conclusions: Our results provide valuable insight into the bacterial component of the termite gut system and significantly expand the inventory of termite prokaryotic genes participating in the deconstruction of plant biomass.

scholarly journals Standing Vegetation Exceeds Soil Microbial Communities in Soil Type Indication: A Procrustes Test of Four Salt-Affected Pastures

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1652
Author(s):  
Péter Csontos ◽  
Márton Mucsi ◽  
Péter Ragályi ◽  
Júlia Tamás ◽  
Tibor Kalapos ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Life Histories ◽  
Environmental Changes ◽  
Soil Microbial Communities ◽  
Chemical Properties ◽  
Principal Component ◽  
Procrustes Analysis ◽  
Soil Conditions ◽  
Habitat Conditions ◽  
Soil Microbial

Organisms with different life histories are able to act as indicators of different characteristics of their environment. Here, we compared the precision of habitat indication by the vegetation and soil microbial communities in four salt-affected pastures: annual open salt sward, Pannonic Puccinellia limosa hollow, Artemisia saline puszta and grassy saline puszta. Dissimilarity of habitats was evaluated by standardized principal component analysis (PCA) based on four different datasets: catabolic profiles of microbial communities in June (a) and September (b), composition of vascular vegetation (c) and physical and chemical properties of the soil (d). Procrustes analysis was used to quantify the resemblance between pairs of PCA ordinations based on soil properties (d) and various biotic communities (a, b, c). PCA ordination based on vegetation most closely matched the soil data-based ordination, thus vegetation appears to better indicate habitat conditions than soil microbial communities do. For microbial communities, a better agreement with the soil data-based ordination was reached in September than in June. Most probably, the long-lived sedentary habit of perennial plants in these communities requires adaptation to long-term average habitat conditions. In contrast, short-lived soil microbes can quickly follow environmental changes, thus the composition of soil microbial communities better reflect actual soil conditions.

scholarly journals Niche partitioning of a pathogenic microbiome driven by chemical gradients

2018 ◽  
Vol 4 (9) ◽  
pp. eaau1908 ◽  
Author(s):  
Robert A. Quinn ◽  
William Comstock ◽  
Tianyu Zhang ◽  
James T. Morton ◽  
Ricardo da Silva ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Human Body ◽  
Niche Partitioning ◽  
Antimicrobial Treatment ◽  
Chemical Gradients ◽  
Similar Chemical ◽  
Predictive Understanding ◽  
The Individual ◽  
And Function ◽  
Microbial Systems

Environmental microbial communities are stratified by chemical gradients that shape the structure and function of these systems. Similar chemical gradients exist in the human body, but how they influence these microbial systems is more poorly understood. Understanding these effects can be particularly important for dysbiotic shifts in microbiome structure that are often associated with disease. We show that pH and oxygen strongly partition the microbial community from a diseased human lung into two mutually exclusive communities of pathogens and anaerobes. Antimicrobial treatment disrupted this chemical partitioning, causing complex death, survival, and resistance outcomes that were highly dependent on the individual microorganism and on community stratification. These effects were mathematically modeled, enabling a predictive understanding of this complex polymicrobial system. Harnessing the power of these chemical gradients could be a drug-free method of shaping microbial communities in the human body from undesirable dysbiotic states.

scholarly journals Characteristics of the Soil Microbial Communities in Different Slope Positions along an Inverted Stone Slope in a Degraded Karst Tiankeng

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 474
Author(s):  
Cong Jiang ◽  
Jie Feng ◽  
Su-Feng Zhu ◽  
Wei Shui
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Diversity Index ◽  
Soil Microbial Communities ◽  
Ecological Value ◽  
Soil Microbial ◽  
Wiener Diversity Index ◽  
The Us ◽  
And Function ◽  
Topographic Heterogeneity

The underground forests developed on inverted stone slopes in degraded karst tiankengs are important areas for biodiversity conservation, but the microbial community profiles have not been sufficiently characterized. Thus, we investigated the soil microbial communities at four sites (at the bottom of the slope (BS), in the middle of the slope (MS), in the upper part of the slope (US) and outside the tiankeng (OT)) in the Shenxiantang tiankeng. The dominant phyla in the inverted stone slope were Proteobacteria, Actinobacteria, and Acidobacteria, and the relative abundance were different in different slope positions. The Shannon–Wiener diversity index of the microbial community was significantly greater for the US site than for the MS or BS sites. The metabolism functional pathways (including C/N cycle) were more abundant at the BS site. Total nitrogen and pH were the dominant factors in determining the distribution of the microbial community along an inverted stone slope. These results suggest that topographic heterogeneity can influence the variations in the soil microbial structure, diversity, and function in degraded karst tiankengs and emphasized the ecological value of inverted stone slopes within karst tiankengs.

Scanning tunneling microscopy (STM) of DNA and RNA

1989 ◽  
Vol 47 ◽  
pp. 34-35
Author(s):  
Patricia G. Arscott ◽  
Gil Lee ◽  
Victor A. Bloomfield ◽  
D. Fennell Evans
Keyword(s):  
Molecular Structures ◽  
Inorganic Materials ◽  
Resolving Power ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Form And Function ◽  
Dna And Rna ◽  
Calf Thymus ◽  
And Function ◽  
The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

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