Patterns of bacterial diversity in embryonic capsules of the spotted salamander Ambystoma maculatum: an expanding view of a symbiosis

ABSTRACT The unicellular green alga, Oophila amblystomatis, populates egg capsules of the spotted salamander Ambystoma maculatum. This nutrient-exchange mutualism is widely perceived as a bipartite interaction, but the presence and contributing effects of bacteria to this symbiosis are unknown. We used standard cultivation techniques and amplicon sequencing of the V4/V5 region of 16S rRNA gene to identify and compare diversity of bacterial taxa in embryonic capsules with that in the aquatic breeding habitat. Our sampling regime allowed us to investigate diversity among individual capsules of an egg mass and between two ponds and sampling years. Capsules contain much lower diversity of bacteria than pond water, and spatial and temporal variation in intracapsular and pond bacterial diversity was observed. Despite this variation, sequences corresponding to species in the orders Burkholderiales and Oligoflexales were either prevalent or abundant, or both. Isolates most commonly recovered from capsules were closely related to species in the genus Herbaspirillum (Burkholderiaceae); other isolates were pseudomonads, but in all cases are closely related to known vascular plant-associated species. We conclude that, despite observed variation, there are bacterial taxa whose presence is held in common spatially and temporally among capsules and that the symbiosis between O. amblystomatis and A. maculatum may involve these taxa.

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Spatial and Temporal Variation in Microbial Diversity and Community Structure in a Contaminated Mangrove Wetland

Applied Sciences ◽

10.3390/app10175850 ◽

2020 ◽

Vol 10 (17) ◽

pp. 5850

Author(s):

Jiaojiao Ma ◽

Ting Zhou ◽

Chunyu Xu ◽

Dawen Shen ◽

Songjun Xu ◽

...

Keyword(s):

Community Structure ◽

Spatial Variation ◽

Temporal Variation ◽

Bacterial Diversity ◽

Diversity Index ◽

Total Carbon ◽

Spatial And Temporal Variation ◽

Rrna Gene ◽

Mangrove Wetland ◽

Mangrove Soils

Field and laboratory investigations were conducted to characterize bacterial diversity and community structure in a badly contaminated mangrove wetland adjacent to the metropolitan area of a megacity in subtropical China. Next-generation sequencing technique was used for sequencing the V4–V5 region of the 16s rRNA gene on the Illumina system. Collectively, Proteobacteria, Chloroflexi, Planctomycetes, Actinobacteria and Bacteroidetes were the predominant phyla identified in the investigated soils. A significant spatial variation in bacterial diversity and community structure was observed for the investigated mangrove soils. Heavy metal pollution played a key role in reducing the bacterial diversity. The spatial variation in soil-borne heavy metals shaped the spatial variation in bacterial diversity and community structure in the study area. Other environmental factors such as total carbon and total nitrogen in the soils that are affected by seasonal change in temperature could also influence the bacterial abundance, diversity and community structure though the temporal variation was relatively weaker, as compared to spatial variation. The bacterial diversity index was lower in the investigated site than in the comparable reference site with less contaminated status. The community structure in mangrove soils at the current study site was, to a remarkable extent, different from those in the tropical mangrove wetlands around the world.

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Bacterial diversity analysis of pork longissimus lumborum following long term ohmic cooking and water bath cooking by amplicon sequencing of 16S rRNA gene

Meat Science ◽

10.1016/j.meatsci.2016.09.007 ◽

2017 ◽

Vol 123 ◽

pp. 97-104 ◽

Cited By ~ 21

Author(s):

Xiaojing Tian ◽

Wei Wu ◽

Qianqian Yu ◽

Man Hou ◽

Fang Gao ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Amplicon Sequencing ◽

Water Bath ◽

Rrna Gene ◽

Diversity Analysis ◽

Longissimus Lumborum

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Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

10.21203/rs.3.rs-384378/v1 ◽

2021 ◽

Author(s):

Nicole E Adams ◽

Madeleine A Becker ◽

Suzanne Edmands

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Captive Breeding ◽

Interdisciplinary Approach ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sample Collection ◽

Channel Island ◽

Island Fox ◽

Urocyon Littoralis

Abstract Background With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and look at the effects of geography and captivity on the variation in bacterial communities. Results Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Conclusions Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

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Changes in the Bacterial Diversity of Human Milk during Late Lactation Period (Weeks 21 to 48)

Foods ◽

10.3390/foods9091184 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1184

Author(s):

Wendy Marin-Gómez ◽

Mᵃ José Grande ◽

Rubén Pérez-Pulido ◽

Antonio Galvez ◽

Rosario Lucas

Keyword(s):

Bacterial Diversity ◽

Single Mother ◽

Variable Region ◽

Sampling Period ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequencing Analysis ◽

Lactation Period ◽

Relative Abundances ◽

The 16S Rrna Gene

Breast milk from a single mother was collected during a 28-week lactation period. Bacterial diversity was studied by amplicon sequencing analysis of the V3-V4 variable region of the 16S rRNA gene. Firmicutes and Proteobacteria were the main phyla detected in the milk samples, followed by Actinobacteria and Bacteroidetes. The proportion of Firmicutes to Proteobacteria changed considerably depending on the sampling week. A total of 411 genera or higher taxons were detected in the set of samples. Genus Streptococcus was detected during the 28-week sampling period, at relative abundances between 2.0% and 68.8%, and it was the most abundant group in 14 of the samples. Carnobacterium and Lactobacillus had low relative abundances. At the genus level, bacterial diversity changed considerably at certain weeks within the studied period. The weeks or periods with lowest relative abundance of Streptococcus had more diverse bacterial compositions including genera belonging to Proteobacteria that were poorly represented in the rest of the samples.

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Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

Frontiers in Microbiology ◽

10.3389/fmicb.2021.748323 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nicole E. Adams ◽

Madeleine A. Becker ◽

Suzanne Edmands

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Captive Breeding ◽

Interdisciplinary Approach ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sample Collection ◽

Channel Island ◽

Island Fox ◽

Urocyon Littoralis

With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and examine the effects of geography and captivity on the variation in bacterial communities. Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

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Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

10.1101/381798 ◽

2018 ◽

Cited By ~ 1

Author(s):

Pablo de Jesús Suárez-Moo ◽

Andrew P. Vovides ◽

M. Patrick Griffith ◽

Francisco Barona-Gómez ◽

Angélica Cibrián-Jaramillo

Keyword(s):

Bacterial Diversity ◽

Natural Populations ◽

Amplicon Sequencing ◽

Botanical Garden ◽

Taxonomic Composition ◽

Rrna Gene ◽

Biological Interactions ◽

Plant Growth Promoting ◽

Coralloid Roots ◽

Root Microbiome

AbstractCycads are among the few plants that have developed specialized roots to host nitrogen-fixing bacteria. We describe the bacterial diversity of the coralloid roots from sevenDioonspecies and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species ofDioonthat we evaluated, suggesting a recent divergence ofDioonpopulations and/or similar plant-driven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched withNostocspp andCalothrixspp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.

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Highly parallelized microfluidic droplet cultivation and prioritization on antibiotic producers from complex natural microbial communities

10.1101/2019.12.18.877530 ◽

2019 ◽

Author(s):

Lisa Mahler ◽

Sarah Niehs ◽

Karin Martin ◽

Thomas Weber ◽

Kirstin Scherlach ◽

...

Keyword(s):

Antimicrobial Activity ◽

Natural Products ◽

Bacterial Diversity ◽

High Throughput ◽

High Throughput Screening ◽

Single Cells ◽

Amplicon Sequencing ◽

Droplet Microfluidics ◽

Rrna Gene ◽

Bacterial Strains

AbstractTo investigate the overwhelming part of the bacterial diversity still evading standard cultivation for its potential use in antibiotic synthesis, we have compiled a microscale-cultivation and screening system. We devised a strategy based on droplet-microfluidics taking advantage of the inherent miniaturization and high throughput. Single cells of natural samples were confined in 9 x 106 aqueous droplets and subjected to long-term incubation under controlled conditions. Subsequent a high-throughput screening for antimicrobial natural products was implemented, employing a whole cell reporting system using the viability of reporter strains as a probe for antimicrobial activity. Due to the described microscale cultivation a novel subset of bacterial strains was made available for the following screening for antimicrobials. We demonstrate the merits of the in-droplet cultivation by comparing the cultivation outcome in microfluidic droplets and on conventional agar plates for a bacterial community derived from soil by 16S rRNA gene amplicon sequencing. In-droplet cultivation resulted in a significantly higher bacterial diversity without the common overrepresentation of Firmicutes. Natural strains able to inhibit either a Gram-positive or a Gram-negative reporter strain were isolated from the microscale system and further cultivated. Thereby a variety of rare isolates was obtained. The natural products with antimicrobial activity were elucidated for the most promising candidate. Our method combines a new cultivation approach with a high-throughput search for antibiotic producers to increase the chances of finding new lead substances.

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Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing

Microbiology Resource Announcements ◽

10.1128/mra.00257-21 ◽

2021 ◽

Vol 10 (19) ◽

Author(s):

Nikola Palevich ◽

Paul H. Maclean ◽

Luis Carvalho ◽

Ruy Jauregui

Keyword(s):

New Zealand ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Sequence Data ◽

Amplicon Sequencing ◽

Lucilia Sericata ◽

Rrna Gene ◽

Data Set ◽

Content Type

ABSTRACT Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult Lucilia sericata, collected from Ashhurst, New Zealand (May 2020). The two dominant genera among adult male and female L. sericata were Serratia and Morganella (phylum Proteobacteria), while the larvae were also dominated by the genera Lactobacillus, Carnobacterium, and Lactococcus (phylum Firmicutes).

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