scholarly journals Phylogenetic conservation of soil bacterial responses to simulated global changes

2020 ◽  
Vol 375 (1798) ◽  
pp. 20190242 ◽  
Author(s):  
Kazuo Isobe ◽  
Nicholas J. Bouskill ◽  
Eoin L. Brodie ◽  
Erika A. Sudderth ◽  
Jennifer B. H. Martiny

Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO 2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yu-Te Lin ◽  
Yu-Fei Lin ◽  
Isheng J. Tsai ◽  
Ed-Haun Chang ◽  
Shih-Hao Jien ◽  
...  

2021 ◽  
Vol 309 ◽  
pp. 107285
Author(s):  
Mengyu Gao ◽  
Jinfeng Yang ◽  
Chunmei Liu ◽  
Bowen Gu ◽  
Meng Han ◽  
...  

mBio ◽  
2014 ◽  
Vol 5 (4) ◽  
Author(s):  
Y. Verastegui ◽  
J. Cheng ◽  
K. Engel ◽  
D. Kolczynski ◽  
S. Mortimer ◽  
...  

ABSTRACTSoil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or stable-isotope-labeled (13C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa,Actinomycetales(Salinibacterium),Rhizobiales(Devosia),Rhodospirillales(Telmatospirillum), andCaulobacterales(PhenylobacteriumandAsticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. BothActinomycetalesandCaulobacterales(Phenylobacterium) were associated with metabolism of cellulose, andAlphaproteobacteriawere associated with the metabolism of arabinose; members of the orderRhizobialeswere strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the13C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes.IMPORTANCEThe ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential.


CATENA ◽  
2022 ◽  
Vol 209 ◽  
pp. 105828
Author(s):  
Chao Yang ◽  
Kangjia Li ◽  
Jipeng Sun ◽  
Weiyi Ye ◽  
Hao Lin ◽  
...  

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