Bacterial metataxonomic profile and putative functional behavior associated with C and N cycle processes remain altered for decades after forest harvest

Mushinski, Ryan M.; Zhou, Yuehan; Gentry, Terry J.; Boutton, Thomas W.

doi:10.1016/j.soilbio.2018.01.008

Cited by 46 publications

(11 citation statements)

References 71 publications

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“…Putative functional genes involved in N transformations were also predicted using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) ( Langille et al, 2013 ), which applies 16S rRNA gene to predict the abundance of functional genes by matching sample OTUs with reference genomes. This gene-based computational approach for assessing ecological functions has been used in various environments, including soil ( Voogd et al, 2015 ; Zarraonaindia et al, 2015 ; Ashworth et al, 2017 ; Mushinski et al, 2018 ). Bacterial OTUs with genes of specific N transformations were also collected with the metagenome_contributions.py script based on Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) database.…”

Section: Methodsmentioning

confidence: 99%

Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa

et al. 2018

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Soil microbes have critical influence on the productivity and sustainability of agricultural ecosystems, yet the magnitude and direction to which management practices affect the soil microbial community remain unclear. This work aimed to examine the impacts of three farming systems, conventional grain cropping (CON), organic grain cropping (ORG), and grain cropping-pasture rotation (ICL), on the soil microbial community structure and putative gene abundances of N transformations using high-throughput 16S rRNA gene and ITS sequencing approaches. Two additional systems, a forest plantation (PF) and an abandoned agricultural field subject to natural succession (SUC), were also included for better assessment of the soil microbial community in terms of variation scale and regulatory importance of management intensity vs. plant type. Farming systems significantly affected the biodiversity of soil fungi but not bacteria, with Shannon index being the lowest in ORG. Bacterial and fungal communities in three cropping systems clustered and separated from those in PF and SUC, suggesting that management practices as such played minor roles in shaping the soil microbial community compared to plant type (i.e., woody vs. herbaceous plants). However, management practices prominently regulated habitat-specific taxa. Lecanoromycetes, a class of Ascomycota accounted for ∼10% of total fungal population in ORG, but almost nil in the other four systems. ORG also enriched bacteria belonging to the phyla, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Gemmatimonadetes. Further, PICRUSt predicted that N-cycle community compositions varied with farming systems; compared to CON, ORG and ICL were more divergent from PF and SUC. Soil pH, together with inorganic N, extractable organic C, and soil organic C:N ratio explained < 50% of the total variations in both bacterial and fungal communities. Our data indicates that while moderately affecting the overall structure of the soil microbial community, management practices, particularly fertilization and the source of N (synthetic vs. organic), were important in regulating the presence and abundance of habitat-specific taxa.

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Section: Methodsmentioning

confidence: 99%

Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa

et al. 2018

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“…Acidobacteria represents an enigmatic phylum with its members copiously distributed in different ecosystems (Mushinski et al, 2018). Acidobacteria is ubiquitous in diverse terrestrial environments ranging from tundra soils to desert soils, from peatland soils and sediments to grasslands, forests, and agricultural lands (Janssen, 2006;Eichorst et al, 2018) and constitute about 5-70% of the soil microbial populace (Huber et al, 2016).…”

Section: Underexplored Phylum Acidobacteriamentioning

confidence: 99%

Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review

et al. 2020

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Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.

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“…2018, Mushinski, Zhou, et al. 2018). In particular, some previous studies, including our own, show higher bacterial α diversity and higher relative abundance of r‐selected bacteria in previously disturbed forest sites (Zhou and Wang 2018, Osburn et al.…”

Section: Introductionmentioning

confidence: 99%

Emergent properties of microbial communities drive accelerated biogeochemical cycling in disturbed temperate forests

Osburn

Badgley

Strahm

et al. 2021

Ecology

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Despite ever‐increasing availability of detailed information about microbial community structure, relationships of microbial diversity with ecosystem functioning remain unclear. We investigated these relationships at the Coweeta Hydrologic Laboratory, where past forest disturbances (e.g., clear‐cut) have altered both ecosystem processes (e.g., increased N export) and microbial communities (e.g., increased bacterial diversity). We sampled soils from disturbed and adjacent reference forests, characterized resident microbial communities, and measured several microbial C‐cycle and N‐cycle process rates. Microbial communities from historically disturbed soils exhibited altered ecosystem functioning, including generally higher rates of C‐ and N‐cycle processes. Disturbed soil microbial communities also exhibited altered ecosystem multifunctionality, a composite variable consisting of all measured process rates as well as extracellular enzyme activities. Although we found few relationships between ecosystem functions and microbial alpha diversity, all functions were correlated with microbial community composition metrics, particularly r:K strategist ratios of bacterial phyla. Additionally, for both ecosystem multifunctionality and specific processes (i.e., C‐ and N‐mineralization), microbial metrics significantly improved models seeking to explain variation in process rates. Our work sheds light on the links between microbial communities and ecosystem functioning and identifies specific microbial metrics important for modeling ecosystem responses to environmental change.

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Bacterial metataxonomic profile and putative functional behavior associated with C and N cycle processes remain altered for decades after forest harvest

Cited by 46 publications

References 71 publications

Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa

Eighteen-Year Farming Management Moderately Shapes the Soil Microbial Community Structure but Promotes Habitat-Specific Taxa

Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review

Emergent properties of microbial communities drive accelerated biogeochemical cycling in disturbed temperate forests

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