Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems – focus on the pelagic environment

Abstract Background One of the central objectives of microbial ecology is to study the distribution of microbial communities and their association with their environments. Biogeographical studies have partitioned the oceans into provinces and regions, but the identification of their boundaries remains challenging, hindering our ability to study transition zones (i.e. ecotones) and microbial ecosystem heterogeneity. Fuzzy clustering is a promising method to do so, as it creates overlapping sets of clusters. The outputs of these analyses thus appear both structured (into clusters) and gradual (due to the overlaps), which aligns with the inherent continuity of the pelagic environment, and solves the issue of defining ecosystem boundaries. Results We show the suitability of applying fuzzy clustering to address the patchiness of microbial ecosystems, integrating environmental (Sea Surface Temperature, Salinity) and bacterioplankton data (Operational Taxonomic Units (OTUs) based on 16S rRNA gene) collected during six cruises over 1.5 years from the subtropical frontal zone off New Zealand. The technique was able to precisely identify ecological heterogeneity, distinguishing both the patches and the transitions between them. In particular we show that the subtropical front is a distinct, albeit transient, microbial ecosystem. Each water mass harboured a specific microbial community, and the characteristics of their ecotones matched the characteristics of the environmental transitions, highlighting that environmental mixing lead to community mixing. Further explorations into the OTU community compositions revealed that, although only a small proportion of the OTUs explained community variance, their associations with given water mass were consistent through time. Conclusion We demonstrate recurrent associations between microbial communities and dynamic oceanic features. Fuzzy clusters can be applied to any ecosystem (terrestrial, human, marine, etc) to solve uncertainties regarding the position of microbial ecological boundaries and to refine the relation between the distribution of microorganisms and their environment.

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Marine Fe-oxidizingZetaproteobacteria: Historical, ecological, and genomic perspectives

10.1101/416842 ◽

2018 ◽

Cited By ~ 3

Author(s):

Sean M. McAllister ◽

Ryan M. Moore ◽

Amy Gartman ◽

George W. Luther ◽

David Emerson ◽

...

Keyword(s):

Hydrothermal Vents ◽

Steel Corrosion ◽

Coastal Sediments ◽

Model Organisms ◽

Rrna Gene ◽

Transition Zones ◽

Operational Taxonomic Units ◽

Fe Oxidation ◽

Subsurface Environments ◽

Attachment Structures

AbstractTheZetaproteobacteriaare a class of bacteria typically associated with marine Fe oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe oxidation. In addition to deep sea and shallow hydrothermal vents,Zetaproteobacteriaare found in coastal sediments, other marine subsurface environments, steel corrosion biofilms, as well as saline terrestrial aquifers and springs. Isolates from a range of environments all grow by Fe oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe oxidation at the low O2concentrations common to Fe(II)-rich oxic/anoxic transition zones. Also,Zetaproteobacteriamake a variety of biomineral morphologies as a repository for Fe(III) waste, and as attachment structures. To determine the known diversity of theZetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While someZetaproteobacteriataxa appear to be cosmopolitan, various habitats enrich for different sets ofZetaproteobacteria. OTU networks show that certainZetaproteobacteriaco-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2, and nitrate availability, based on genomic analyses. Also, a putative Fe oxidation gene has been found in diverseZetaproteobacteriataxa, suggesting that theZetaproteobacteriaevolved as specialists in Fe oxidation. In all, culture, genomic, and environmental studies suggest thatZetaproteobacteriaare widespread, and therefore have a broad influence on marine and saline terrestrial Fe cycling.

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PSII-16 Evidence for stratification of rumen wall microbial communities revealed by 16S rRNA based amplicon sequencing

Journal of Animal Science ◽

10.1093/jas/skz122.398 ◽

2019 ◽

Vol 97 (Supplement_2) ◽

pp. 226-227

Author(s):

Lucas Koester ◽

Mark Lyte ◽

Stephan Schmitz-Esser ◽

Heather Allen

Keyword(s):

16S Rrna ◽

Microbial Communities ◽

Temporal Stability ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Rumen Content ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Abundant Otus ◽

Dorsal Portion

Abstract Rumen content (RC) stratifies based on particle size and density consisting of the less dense forage within the dorsal and the denser particles in the ventral portions of the rumen and is in constant contact with the microbial communities present on the rumen wall (RW) epithelium. Little is known about the nutrient requirements and functional processes of RW microbial communities. Our hypothesis is that the RW microbial communities stratify mirroring the stratification of RC due to different available nutrients. Five fistulated, milking Holstein cows of the same management conditions were sampled at four rumen layers corresponding to the RC stratification. Epithelial biopsies were taken through the fistula; the uppermost aligned with the dorsal portion of the RC (A), and three other sites, each 10 cm ventral to the previous (B, C and D). Each cow and stratification layer was sampled five times over four months to analyze temporal stability of the RW microbial communities. DNA was extracted using the Qiagen Powerlyzer Powersoil kit and used for 16S rRNA gene Illumina MiSeq sequencing. Sequences were clustered into operational taxonomic units (OTU) based on a 99% similarity cutoff using MOTHUR. After quality control, 2.0 million reads remained for 90 samples which were clustered into 5,016 OTUs with 10 or more reads. 99.2% of the reads were bacterial, whereas 0.8% affiliated to Archaea. Statistical analysis revealed that among the 20 most abundant OTUs, phylotypes classified as Desulfobulbus, unclassified_Cardiobacteraceae, Mogibacterium, Lachnospiraceae-UCG008 and Methanobrevibacter were significantly different in abundance between sites A compared to D. On a whole community level, analysis of molecular variance (AMOVA) revealed significant differences between groups A, C and D. Our data reveal first evidence that a stratification of RW microbiota is present in dairy cattle and also reveal high temporal stability of RW microbiota.

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Microbiome of Grand Canyon Caverns, a dry sulfuric karst cave in Arizona, supports diverse extremo-philic bacterial and archaeal communities

Journal of Cave and Karst Studies ◽

10.4311/2019mb0126 ◽

2021 ◽

Vol 83 (1) ◽

pp. 44-56

Author(s):

Raymond Keeler ◽

Bradley Lusk

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Grand Canyon ◽

Rrna Gene ◽

Karst Cave ◽

Operational Taxonomic Units ◽

Karst Caves ◽

Bacterial And Archaeal Communities ◽

Karst Systems

We analyzed the microbial community of multicolored speleosol deposits found in Grand Canyon Caverns, a dry sulfuric karst cave in northwest Arizona, USA. Underground cave and karst systems harbor a great range of microbial diversity; however, the inhabitants of dry sulfuric karst caves, including extremophiles, remain poorly understood. Understanding the microbial communities inhabiting cave and karst systems is essential to provide information on the multidirectional feedback between biology and geology, to elucidate the role of microbial biogeochemical processes on cave formation, and potentially aid in the development of biotechnology and pharmaceuticals. Based on the V4 region of the 16S rRNA gene, the microbial community was determined to consist of 2207 operational taxonomic units (OTUs) using species-level annotations, representing 55 phyla. The five most abundant Bacteria were Actinobacteria 51.3 ± 35.4 %, Proteobacteria 12.6 ± 9.5 %, Firmicutes 9.8 ± 7.3 %, Bacteroidetes 8.3 ± 5.9 %, and Cyanobacteria 7.1 ± 7.3 %. The relative abundance of Archaea represented 1.1 ± 0.9 % of all samples and 0.2 ± 0.04 % of samples were unassigned. Elemental analysis found that the composition of the rock varied by sample and that calcium (6200 ± 3494 ppm), iron (1141 ± 1066 ppm), magnesium (25 ± 17 ppm), and phosphorous (37 ± 33 ppm) were the most prevalent elements detected across all samples. Furthermore, carbon, hydrogen, and nitrogen were found to compose 4.7 ± 4.9 %, 0.3 ± 0.4 %, and 0.1 ± 0.1 % of samples, respectively. Finally, Raman spectra compared to the RRUFF Project database using CrystalSleuth found that the mineral composition of the speleosol consisted of calcite, hematite, paraspurrite, quartz, and trattnerite. These data suggest that dry sulfuric karst caves can harbor robust microbial communities under oligotrophic, endolithic, and troglophilic conditions.

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Dietary bovine milk exosomes elicit changes in bacterial communities in C57BL/6 mice

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00160.2019 ◽

2019 ◽

Vol 317 (5) ◽

pp. G618-G624 ◽

Cited By ~ 15

Author(s):

Fang Zhou ◽

Henry A. Paz ◽

Mahrou Sadri ◽

Juan Cui ◽

Stephen D. Kachman ◽

...

Keyword(s):

Microbial Communities ◽

Gut Microbiome ◽

Bacterial Communities ◽

Bovine Milk ◽

Cell Communication ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

The Family ◽

Rrna Gene Sequencing

Exosomes and exosome-like vesicles participate in cell-to-cell communication in animals, plant, and bacteria. Dietary exosomes in bovine milk are bioavailable in nonbovine species, but a fraction of milk exosomes reaches the large intestine. We hypothesized that milk exosomes alter the composition of the gut microbiome in mice. C57BL/6 mice were fed AIN-93G diets, defined by their content of bovine milk exosomes and RNA cargos: exosome/RNA-depleted (ERD) versus exosome/RNA-sufficient (ERS) diets. Feeding was initiated at age 3 wk, and cecum content was collected at ages 7, 15, and 47 wk. Microbial communities were identified by 16S rRNA gene sequencing. Milk exosomes altered bacterial communities in the murine cecum. The abundance of three phyla, seven families, and 52 operational taxonomic units (OTUs) was different in the ceca from mice fed ERD and ERS ( P < 0.05). For example, at the phylum level, Tenericutes had more than threefold abundance in ERS mice at ages 15 and 47 wk compared with ERD mice ( P < 0.05). At the family level, Verrucomicrobiaceae were much less abundant in ERS mice compared with ERD mice age 47 wk ( P < 0.05). At the OTU level, four OTUs from the family of Lachnospiraceae were more than two times more abundant in ERS mice compared with ERD at age 7 and 47 wk ( P < 0.05). We conclude that exosomes in bovine milk alter microbial communities in nonbovine species, suggesting that exosomes and their cargos participate in the crosstalk between bacterial and animal kingdoms. NEW & NOTEWORTHY This is the first report that exosomes from bovine milk alter microbial communities in mice. This report suggests that the gut microbiome facilitates cell-to-cell communication by milk exosomes across species boundaries, and milk exosomes facilitate communication across animal and bacteria kingdoms.

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Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China

PeerJ ◽

10.7717/peerj.6044 ◽

2018 ◽

Vol 6 ◽

pp. e6044 ◽

Cited By ~ 2

Author(s):

Yan Zhu ◽

Yingying Cao ◽

Min Yang ◽

Pengchen Wen ◽

Lei Cao ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Diversity ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Microbial Interactions ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Different Origins ◽

Different Levels ◽

Different Origin

Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3–V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology.

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TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

10.1101/214288 ◽

2017 ◽

Cited By ~ 6

Author(s):

Robin R. Rohwer ◽

Joshua J. Hamilton ◽

Ryan J. Newton ◽

Katherine D. McMahon

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Microbial Community Composition ◽

Taxonomic Resolution ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Comprehensive Database ◽

Reference Databases ◽

Fine Resolution

ABSTRACTTaxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater datasets using the comprehensive Silva database and the freshwater-specific FreshTrain database. TaxAss increased the percent of the dataset classified compared to using only Silva, especially at fine-resolution family-species taxa levels, while across the freshwater test-datasets classifications increased by as much as 11-40 percent of total reads. A similar increase in classifications was not observed in a control mouse gut dataset, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxa-levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxa levels incorrect classifications became significant. We validated TaxAss using simulated amplicon data with known taxonomy and found that 96-99% of test sequences were correctly classified at fine resolution. TaxAss splits a dataset’s sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source, and available at www.github.com/McMahonLab/TaxAss.IMPORTANCEMicrobial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon datasets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at phylum, class, and order level lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are dataset-dependent and cannot be compared between datasets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between datasets.

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OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

mSphere ◽

10.1128/mspheredirect.00073-17 ◽

2017 ◽

Vol 2 (2) ◽

Cited By ~ 167

Author(s):

Sarah L. Westcott ◽

Patrick D. Schloss

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Significant Advance ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Operational Taxonomic Units ◽

Taxonomic Groups

ABSTRACT Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here, we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to 10 other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6 times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the data set. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications. IMPORTANCE The analysis of microbial communities from diverse environments using 16S rRNA gene sequencing has expanded our knowledge of the biogeography of microorganisms. An important step in this analysis is the assignment of sequences into taxonomic groups based on their similarity to sequences in a database or based on their similarity to each other, irrespective of a database. In this study, we present a new algorithm for the latter approach. The algorithm, OptiClust, seeks to optimize a metric of assignment quality by shuffling sequences between taxonomic groups. We found that OptiClust produces more robust assignments and does so in a rapid and memory-efficient manner. This advance will allow for a more robust analysis of microbial communities and the factors that shape them. Podcast: A podcast concerning this article is available.

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Overlapping Community Compositions of Gut and Fecal Microbiomes in Lab-Reared and Field-Collected German Cockroaches

Applied and Environmental Microbiology ◽

10.1128/aem.01037-18 ◽

2018 ◽

Vol 84 (17) ◽

Cited By ~ 15

Author(s):

Madhavi L. Kakumanu ◽

Julia M. Maritz ◽

Jane M. Carlton ◽

Coby Schal

Keyword(s):

Microbial Communities ◽

Microbial Community Composition ◽

18S Rrna Gene ◽

Rrna Gene ◽

Content Type ◽

Fecal Microbiome ◽

Operational Taxonomic Units ◽

Overlapping Community ◽

Next Generation Sequencing Ngs ◽

The Relationship

ABSTRACTGerman cockroaches,Blattella germanica(Blattodea: Ectobiidae), are human commensals that move freely between food and waste, disseminating bacteria, including potential pathogens, through their feces. However, the relationship between the microbial communities of the cockroach gut and feces is poorly understood. We analyzed the V4 region of the 16S rRNA gene and the V9 region of the 18S rRNA gene by next-generation sequencing (NGS) to compare the bacterial and protist diversities in guts versus feces and males versus females, as well as assess variation across cockroach populations. Cockroaches harbored a diverse array of bacteria, and 80 to 90% of the operational taxonomic units (OTUs) were shared between the feces and gut. Lab-reared and field-collected cockroaches had distinct microbiota, and whereas lab-reared cockroaches had relatively conserved communities, considerable variation was observed in the microbial community composition of cockroaches collected in different apartments. Nonetheless, cockroaches from all locations shared some core bacterial taxa. The eukaryotic community in the feces of field-collected cockroaches was found to be more diverse than that in lab-reared cockroaches. These results demonstrate that cockroaches disseminate their gut microbiome in their feces, and they underscore the important contribution of the cockroach fecal microbiome to the microbial diversity of cockroach-infested homes.IMPORTANCEThe German cockroach infests diverse human-built structures, including homes and hospitals. It produces potent allergens that trigger asthma and disseminates opportunistic pathogens in its feces. A comprehensive understanding of gut and fecal microbial communities of cockroaches is essential not only to understand their contribution to the biology of the cockroach, but also for exploring their clinical relevance. In this study, we compare the diversity of bacteria and eukaryotes in the cockroach gut and feces and assess the variation in the gut microbiota across cockroach populations.

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A Comparative Study on the Microbial Communities of Rhynchophorus ferrugineus (Red Palm Weevil)-Infected and Healthy Palm Trees

Arabian Journal for Science and Engineering ◽

10.1007/s13369-021-05979-9 ◽

2021 ◽

Author(s):

N. Alshammari ◽

Meshari Alazmi ◽

Naimah A. Alanazi ◽

Abdel Moneim E. Sulieman ◽

Vajid N. Veettil ◽

...

Keyword(s):

Microbial Communities ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Rhynchophorus Ferrugineus ◽

Tree Trunk ◽

Red Palm Weevil ◽

Healthy Tree ◽

Palm Trees ◽

Infected Tree ◽

Palm Weevil

AbstractSeveral studies have investigated palm trees’ microbiota infected with red palm weevil (RPW) (Rhynchophorus ferrugineus), the major pest of palm trees. This study compared the microbial communities of infected and uninfected palm trees in the Hail region, Northern Saudi Arabia, determined by high-throughput 16S rRNA gene sequencing by Illumina MiSeq. The results indicated that taxonomic diversity variation was higher for infected tree trunk than the healthy tree trunk. Soil samples from the vicinity of healthy and infected trees did not have a significant variation in bacterial diversity. Myxococcota, Acidobacteriota, and Firmicutes were the dominant phyla in RPW-infected tree trunk, and Pseudomonadaceae was the most prominent family. This study is the first report on the characterization of RPW-infected and healthy palm trees’ microbiome.

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Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽

10.3390/fuels2020014 ◽

2021 ◽

Vol 2 (2) ◽

pp. 241-252

Author(s):

Dyah Asri Handayani Taroepratjeka ◽

Tsuyoshi Imai ◽

Prapaipid Chairattanamanokorn ◽

Alissara Reungsang

Keyword(s):

Microbial Communities ◽

High Throughput ◽

High Throughput Sequencing ◽

High Salinity ◽

Amplicon Sequencing ◽

Spatial Proximity ◽

Lignocellulosic Waste ◽

Evaporation Pond ◽

Operational Taxonomic Units ◽

Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

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