Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea)

Abstract Background Microbial transmission from parent to offspring is hypothesized to be widespread in vertebrates. However, evidence for this is limited as many evolutionarily important clades remain unexamined. There is currently no data on the microbiota associated with any Chondrichthyan species during embryonic development, despite the global distribution, ecological importance, and phylogenetic position of this clade. In this study, we take the first steps towards filling this gap by investigating the microbiota associated with embryonic development in the little skate, Leucoraja erinacea, a common North Atlantic species and popular system for chondrichthyan biology. Methods To assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, at six points during ontogeny. Community composition was analyzed using the QIIME2 pipeline and microbial continuity between stages was tracked using FEAST. Results We identify site-specific and stage-specific microbiota dominated by the bacterial phyla Proteobacteria and Bacteroidetes. This composition is similar to, but distinct from, that of previously published data on the adult microbiota of other chondrichthyan species. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop. Conclusions Our study is the first exploration of the chondrichthyan microbiota throughout ontogeny and provides the first evidence of vertical transmission in this group.

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Intergenerational microbial transmission in the little skate (Leucoraja erinacea)

10.1101/2020.12.30.424594 ◽

2020 ◽

Author(s):

Katelyn Mika ◽

Alexander S. Okamoto ◽

Neil H. Shubin ◽

David B. Mark Welch

Keyword(s):

Bacterial Communities ◽

Internal Surface ◽

Amplicon Sequencing ◽

Site Specific ◽

Bacterial Phyla ◽

16S Rrna Amplicon Sequencing ◽

Primary Mechanism ◽

Bacterial Transmission ◽

Embryonic Skin ◽

Egg Capsule

AbstractMicrobial transmission from parent to offspring is hypothesized to be universal in vertebrates. However, evidence for this is limited as many clades remain unexamined. Chondrichthyes, as one of the earliest–branching vertebrate lineages, provide an opportunity to investigate the phylogenetic breadth of this hypothesis. To assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, Leucoraja erinacea, at six points during ontogeny. We identify site-specific microbiomes dominated by the bacterial phyla Proteobacteria and Bacteroidetes, a composition similar to, but distinct from, that of other chondrichthyans. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop. Our study is the first exploration of the chondrichthyan microbiome throughout ontogeny and provides the first evidence of vertical transmission in this group, which may be the primary mechanism for the signature of phylosymbiosis previously observed in elasmobranchs.

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Dynamic succession of substrate-associated bacterial composition and function duringGanoderma lucidumgrowth

PeerJ ◽

10.7717/peerj.4975 ◽

2018 ◽

Vol 6 ◽

pp. e4975 ◽

Cited By ~ 7

Author(s):

Bo Zhang ◽

Lijuan Yan ◽

Qiang Li ◽

Jie Zou ◽

Hao Tan ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Community Dynamics ◽

Bacterial Community Composition ◽

Growth Stages ◽

Bacterial Phyla ◽

Medicinal Fungus ◽

Bacterial Community Dynamics ◽

Functional Pathway ◽

And Function

BackgroundGanoderma lucidum, a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities.MethodsWe analyzed the bacterial community dynamics in the substrate during the four typical growth stages ofG. lucidumusing next-generation sequencing.ResultsThe physicochemical properties of the substrate (e.g. acidity, moisture, total nitrogen, total phosphorus and total potassium) changed between different growth stages. A total of 598,771 sequences from 12 samples were obtained and assigned to 22 bacterial phyla.ProteobacteriaandFirmicuteswere the dominant phyla. Bacterial community composition and diversity significantly differed between the elongation stage and the other three growth stages. LEfSe analysis revealed a large number of bacterial taxa (e.g.Bacteroidetes,AcidobacteriaandNitrospirae) with significantly higher abundance at the elongation stage. Functional pathway prediction uncovered significant abundance changes of a number of bacterial functional pathways between the elongation stage and other growth stages. At the elongation stage, the abundance of the environmental information processing pathway (mainly membrane transport) decreased, whereas that of the metabolism-related pathways increased.DiscussionThe changes in bacterial community composition, diversity and predicted functions were most likely related to the changes in the moisture and nutrient conditions in the substrate with the growth ofG. lucidum, particularly at the elongation stage. Our findings shed light on theG. lucidum-bacteria-substrate relationships, which should facilitate the industrial cultivation ofG. lucidum.

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The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

PLoS ONE ◽

10.1371/journal.pone.0099722 ◽

2014 ◽

Vol 9 (6) ◽

pp. e99722 ◽

Cited By ~ 30

Author(s):

Federico M. Ibarbalz ◽

María Victoria Pérez ◽

Eva L. M. Figuerola ◽

Leonardo Erijman

Keyword(s):

Bacterial Community ◽

Quantitative Assessment ◽

Community Dynamics ◽

Amplicon Sequencing ◽

Bacterial Community Dynamics

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BACTERIAL COMMUNITY SUCCESSION AND INFLUENCING FACTORS OF IMPERATA CYLINDRICA LITTER DECOMPOSITION IN A DEGRADED COPPER TAILINGS DAM OF CHINA

10.22541/au.163257350.09106780/v1 ◽

2021 ◽

Author(s):

Tong Jia ◽

Xiaoxia Liang ◽

Tingyan Guo ◽

Baofeng Chai

Keyword(s):

Bacterial Community ◽

Litter Decomposition ◽

Community Dynamics ◽

Nutrient Content ◽

Driving Factors ◽

Imperata Cylindrica ◽

Community Characteristics ◽

Bacterial Phyla ◽

Bacterial Community Dynamics ◽

Litter Properties

Litter decomposition is a critical component of the ecological nutritional transformation process. It is particularly important to investigate characteristics and interactions of bacterial communities in litter decomposition in heavy metal polluted degrade areas, which will help clarify driving mechanisms of organic matter and nutrient cycling in mining areas that harbor contaminated soil. Imperata cylindrical was the dominant plant species in the degrade area investigated; thus, we selected this species as research object. Here we explore bacterial community characteristics and key microbial groups as well as driving factors of litter decomposition using in-situ litter decomposition experiments. The nutrient content of I. cylindrica decreased, while the litter pH status increased as decomposition progressed in one of the three sub-dams investigated (i.e., S516). Proteobacteria and Actinobacteriota were the dominant bacterial phyla during the different litter decomposition stages. Moreover, the role of Friedmanniella was critical in sustaining both structure and function of the bacterial community during the early decomposition stage. Quadrisphaera became the dominant species as litter decomposition progressed. Litter properties and enzyme activities both had significant effects on litter bacterial community characteristics, whose driving factors varied during different restoration stages. The bacterial community dynamics of litter were affected primarily by litter properties during the decomposition process. Furthermore, the most crucial factors that impacted bacterial litter structure were pH and copper content. Findings will help to deepen our understanding of litter decomposition mechanisms in degraded ecosystems, while also providing a scientific basis for improving effectiveness of material circulation and nutrient transformation in degrade ecosystems.

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