scholarly journals Use of RNA and DNA to Identify Mechanisms of Microbial Community Homogenization

2018 ◽  
Author(s):  
Kyle M Meyer ◽  
Ian A.B. Petersen ◽  
Elie Tobi ◽  
Lisa Korte ◽  
Brendan Bohannan
Keyword(s):  
Land Use ◽  
Community Structure ◽  
Microbial Community ◽  
Environmental Changes ◽  
Environmental Variability ◽  
Congo Basin ◽  
Active Fraction ◽  
Soil Environment ◽  
Inference Methods ◽  
Rna And Dna

Biotic homogenization is a commonly observed response following conversion of native ecosystems to agriculture, but our mechanistic understanding of this process is limited for microbial communities. In the case of rapid environmental changes, inference of homogenization mechanisms may be confounded by the fact that only a minority of taxa is active at any given point. RNA- and DNA-based community inference may help to distinguish the active fraction of a community from inactive taxa. Using these two community inference methods, we asked how soil prokaryotic communities respond to land use change following transition from rainforest to agriculture in the Congo Basin. Our results indicate that the magnitude of community homogenization is larger in the RNA-inferred community than the DNA-inferred perspective. We show that as the soil environment changes, the RNA-inferred community structure tracks environmental variation and loses spatial structure. The DNA-inferred community loses its association with environmental variability. Homogenization of the DNA-inferred community appears to instead be driven by the range expansion of a minority of taxa shared between the forest and conversion sites, which is also seen in the RNA-inferred community. Our results suggest that complementing DNA-based surveys with RNA can provide unique perspectives on community responses to environmental change.

scholarly journals Characterization of Microbial Community Structure in Gulf of Mexico Gas Hydrates: Comparative Analysis of DNA- and RNA-Derived Clone Libraries

2005 ◽  
Vol 71 (6) ◽  
pp. 3235-3247 ◽  
Author(s):  
Heath J. Mills ◽  
Robert J. Martinez ◽  
Sandra Story ◽  
Patricia A. Sobecky
Keyword(s):  
Phylogenetic Analysis ◽  
Microbial Community ◽  
Gulf Of Mexico ◽  
Gas Hydrate ◽  
Phylogenetic Analyses ◽  
Active Fraction ◽  
Clone Libraries ◽  
Dna And Rna ◽  
Rna And Dna

ABSTRACT The characterization of microbial assemblages within solid gas hydrate, especially those that may be physiologically active under in situ hydrate conditions, is essential to gain a better understanding of the effects and contributions of microbial activities in Gulf of Mexico (GoM) hydrate ecosystems. In this study, the composition of the Bacteria and Archaea communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA extracted from sediment-entrained hydrate (SEH) and interior hydrate (IH). The hydrate was recovered from an exposed mound located in the northern GoM continental slope with a hydrate chipper designed for use on the manned-submersible Johnson Sea Link (water depth, 550 m). Previous geochemical analyses indicated that there was increased metabolic activity in the SEH compared to the IH layer (B. N. Orcutt, A. Boetius, S. K. Lugo, I. R. Macdonald, V. A. Samarkin, and S. Joye, Chem. Geol. 205:239-251). Phylogenetic analysis of RNA- and DNA-derived clones indicated that there was greater diversity in the SEH libraries than in the IH libraries. A majority of the clones obtained from the metabolically active fraction of the microbial community were most closely related to putative sulfate-reducing bacteria and anaerobic methane-oxidizing archaea. Several novel bacterial and archaeal phylotypes for which there were no previously identified closely related cultured isolates were detected in the RNA- and DNA-derived clone libraries. This study was the first phylogenetic analysis of the metabolically active fraction of the microbial community extant in the distinct SEH and IH layers of GoM gas hydrate.

Land use change in Amazonian Dark Earth and Acrisol: Responses of organic carbon, organic matter composition and microbial carbon utilisation

2020 ◽  
Author(s):  
Klaus Jarosch ◽  
Luis Carlos Colocho Hurtarte ◽  
Konstantin Gavazov ◽  
Aleksander Westphal Muniz ◽  
Christoph Müller ◽  
...  
Keyword(s):  
Land Use ◽  
Organic Matter ◽  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Land Use Change ◽  
Microbial Community Structure ◽  
Secondary Forest ◽  
Soil Types ◽  
Amazonian Dark Earth

<p>The conversion of tropical forest for cassava cultivation is widely known to decrease the soil organic matter (OM) and nutrient contents of highly weathered soils in the tropics. Amazonian Dark Earth (ADE) might be affected less due to their historical anthropogenic amelioration with e.g. charcoal, ceramics and bones, leading to higher soil OM and nutrient concentrations. In this study, we analysed the effect of land use change on the OM dynamics and its composition under tropical conditions, using ADE and an adjacent Acrisol (ACR) as model systems. Soil samples were obtained south of Manaus (Brazil), from a secondary forest and an adjacently located 40-year-old cassava plantation. The land use change induced a severe decrease of organic carbon (OC) concentrations in ADE (from 35 to 15 g OC kg<sup>‑1</sup>) while OC in the adjacent ACR was less affected (18 to 16 g OC kg<sup>‑1</sup>). Soils were analysed by <sup>13</sup>C NMR spectroscopy to obtain information on how the conversion of secondary forest to cassava affected the chemical composition of OM. Our results show that land use change induces differences in the OM composition: The OM in ADE changes to a more decomposed state (increase of alkyl:O/N-alkyl ratio) whereas the OM in ACR changes to a less decomposed state (decrease of alkyl:O/N-alkyl ratio). According to a molecular mixing model, land use change influenced mostly the proportion of lipids, which might be related with a change of the plant input. The incubation of the soils with <sup>13</sup>C glucose enabled resolving how soil microorganisms were affected by land use change. In both soil types ADE and ACR, land use change caused a reduction of the total <sup>13</sup>C glucose respiration by approximately one third in a 7-days incubation, implying lower microbial activity. Microorganisms in both soil types appear to be more readily active in soils under forest, since we observed a distinct lag time between <sup>13</sup>C glucose addition and respiration under cassava planation. This indicated differences in microbial community structure, which we will assess further by determining the <sup>13</sup>C label uptake by the microbial biomass and the microbial community structure using <sup>13</sup>C PLFA analysis. Preliminary results from synchrotron-based STXM demonstrate a distinct arrangement of OM at fine-sized charcoal-particle interfaces. Samples of soils receiving <sup>13</sup>C label will be further analysed by NanoSIMS with the hypothesis that charcoal interfaces foster nutrient dynamics at the microscale. Despite the high loss of OC in the ameliorated ADE through land use change, the remaining OM might improve the nutrient availability thanks to charcoal interactions compared to the ACR. Our results contribute to a better understanding of the sensitivity of OM upon land use change and how the microbial community is responding to land use change in highly weathered tropical soils.</p>

scholarly journals Study on the Rhizosphere Soil Microbial Community Structure Associated with Five Land Use Types in Jinchuan Mining Area

2021 ◽  
Vol 237 ◽  
pp. 01010
Author(s):  
Tian-Peng Gao ◽  
Jing-Wen Fu ◽  
Ming-Bo Zuo ◽  
Yu-Bing Liu ◽  
Dang-Hui Xu ◽  
...  
Keyword(s):  
Land Use ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Soil Microbial Community ◽  
Mining Area ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Land Use Types ◽  
Tailing Dam

Five different land use types (desert, farmland, mining park, slag heap and tailing dam) were selected as variables around the Jinchuan Cu-Ni mining area in Jinchang, Gansu Province in the present study. The Atriplex canescens (Pursh) Nutt.’s rhizosphere bacterial abundance, diversity and community composition were examined taking advantage of High-throughput sequencing technology to discuss the effect of soil physicochemical properties on soil microbial community structure. The result indicated that the phylum Proteobacteria and Firmicutes was the most dominant taxon in desert, farmland and mining park, with a high abundance more than 30%. The phylum Proteobacteria was the most dominant taxon in slag heap and tailing dam, with a high abundance more than 40%. The tailing dam had the highest bacterial Chao indexes and the farmland had the highest bacterial Observed species indexes, Shannon indexes and Simpson indexes. Observed species indexes and Shannon indexes between the five sites were significantly different. The redundancy analysis and principal component analysis showed that the main environmental factors caused the different of rhizosphere bacterial community structure in five land use types were Mg, Ca, Cu, TN and moisture, followed by Ni, Cr, K, Pb, Zn content and pH. Hence, the result indicates that land use and soil environmental factors had significant impact on the diversity of soil microbial community structure.

scholarly journals The match between microbial community structure and soil properties is modulated by land use types and sample origin within an integrated agroecosystem

2014 ◽  
Vol 78 ◽  
pp. 97-108 ◽  
Author(s):  
Francy Junio Gonçalves Lisboa ◽  
Guilherme Montandon Chaer ◽  
Marcelo Ferreira Fernandes ◽  
Ricardo Luis Louro Berbara ◽  
Beata Emoke Madari
Keyword(s):  
Land Use ◽  
Community Structure ◽  
Microbial Community ◽  
Soil Properties ◽  
Microbial Community Structure ◽  
Land Use Types

scholarly journals Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Laís F. O. Lima ◽  
Maya Weissman ◽  
Micheal Reed ◽  
Bhavya Papudeshi ◽  
Amanda T. Alker ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Dynamic Model ◽  
Microbial Community Structure ◽  
Environmental Changes ◽  
Mucus Layer ◽  
Shotgun Metagenomics ◽  
Microbial Network ◽  
Coral Microbiome ◽  
Relative Abundances

ABSTRACT Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver. IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa. The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.

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