Introducing TreeClimber, a Test To Compare Microbial Community Structures

ABSTRACT The phylogenetic and ecological complexity of microbial communities necessitates the development of new methods to determine whether two or more communities have the same structure even though it is not possible to sample the communities exhaustively. To address this need, we adapted a method used in population genetics, the parsimony test, to determine the relatedness of communities. Here we describe our implementation of the parsimony test, TreeClimber, in which we reanalyzed six previously published studies and compared the results of the analysis to those obtained using ∫-LIBSHUFF.

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High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

10.21203/rs.3.rs-34433/v1 ◽

2020 ◽

Author(s):

Wu Qu ◽

Boliang Gao ◽

Jie Wu ◽

Min Jin ◽

Jianxin Wang ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Fungal Community ◽

Amplicon Sequencing ◽

Biotic Factors ◽

Community Structures ◽

Mangrove Sediments ◽

Element Cycling ◽

Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

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Variation in Human Milk Composition Is Related to Differences in Milk and Infant Fecal Microbial Communities

Microorganisms ◽

10.3390/microorganisms9061153 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1153

Author(s):

Ryan M. Pace ◽

Janet E. Williams ◽

Bianca Robertson ◽

Kimberly A. Lackey ◽

Courtney L. Meehan ◽

...

Keyword(s):

Microbial Community ◽

Human Milk ◽

Microbial Communities ◽

Geographical Variation ◽

Milk Composition ◽

Published Data ◽

Community Structures ◽

Microbial Community Structures ◽

Infant Feces ◽

Human Milk Oligosaccharide

Previously published data from our group and others demonstrate that human milk oligosaccharide (HMOs), as well as milk and infant fecal microbial profiles, vary by geography. However, little is known about the geographical variation of other milk-borne factors, such as lactose and protein, as well as the associations among these factors and microbial community structures in milk and infant feces. Here, we characterized and contrasted concentrations of milk-borne lactose, protein, and HMOs, and examined their associations with milk and infant fecal microbiomes in samples collected in 11 geographically diverse sites. Although geographical site was strongly associated with milk and infant fecal microbiomes, both sample types assorted into a smaller number of community state types based on shared microbial profiles. Similar to HMOs, concentrations of lactose and protein also varied by geography. Concentrations of HMOs, lactose, and protein were associated with differences in the microbial community structures of milk and infant feces and in the abundance of specific taxa. Taken together, these data suggest that the composition of human milk, even when produced by relatively healthy women, differs based on geographical boundaries and that concentrations of HMOs, lactose, and protein in milk are related to variation in milk and infant fecal microbial communities.

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Salt stress-induced changes in microbial community structures and metabolic processes result in increased soil cadmium availability

The Science of The Total Environment ◽

10.1016/j.scitotenv.2021.147125 ◽

2021 ◽

Vol 782 ◽

pp. 147125

Author(s):

Meng Wang ◽

Shuwen Zhao ◽

Lifu Wang ◽

Shibao Chen ◽

Shanshan Li ◽

...

Keyword(s):

Salt Stress ◽

Microbial Community ◽

Community Structures ◽

Metabolic Processes ◽

Microbial Community Structures ◽

Soil Cadmium ◽

Induced Changes

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Microbial Population Changes during Bioremediation of an Experimental Oil Spill

Applied and Environmental Microbiology ◽

10.1128/aem.65.8.3566-3574.1999 ◽

1999 ◽

Vol 65 (8) ◽

pp. 3566-3574 ◽

Cited By ~ 373

Author(s):

Sarah J. MacNaughton ◽

John R. Stephen ◽

Albert D. Venosa ◽

Gregory A. Davis ◽

Yun-Juan Chang ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Oil Spill ◽

Phospholipid Fatty Acid ◽

Community Structures ◽

Gram Negative ◽

Dgge Analysis ◽

16S Rdna Pcr ◽

Microbial Community Structures ◽

Plfa Analysis

ABSTRACT Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria andFlexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.

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