Variation in Melitaea cinxia gut microbiota is phylogenetically highly structured but only mildly driven by host plant microbiota, sex or parasitism

Originality-Significance StatementThe factors contributing to the assembly of microbiota in animals are extremely complex, and thus a comprehensive understanding of the mechanisms shaping host-associated microbial communities in natural ecosystems requires extensive ecological studies and appropriate statistical methods. In this study, we investigated the bacterial microbiota associated with the caterpillars of the Glanville fritillary (Melitaea cinxia), which is a long-term-studied ecological model system. We assessed the structure of variation in both occurrence and abundance of gut microbial communities of individuals collected in the wild with joint-species modelling, with the aim to relate the microbial community structure with multiple potentially impacting covariates: host plant microbiota and metabolites, hosts’ sex, potential parasitoid infection, and family structure. These covariates exhibited substantial correlation with multiple microbial taxa’s occurrences, which correlations were consistent for phylogenetically related groups of taxa, but varied across the whole microbial community; on the contrary, only few correlations were found with taxa’s abundances. The dominating co-occurrence pattern of microbiota assembly, which effectively split caterpillar individuals into two distinct groups, was, however, unrelated to any of the considered covariates.SummaryUnderstanding of what ecological factors shape intraspecific variation of insect microbiota is still relatively poor. In Lepidopteran caterpillars, microbiota is assumed to be mainly composed of transient bacterial symbionts acquired from the host plant. We sampled Glanville fritillary (Melitaea cinxia) caterpillars from natural populations to describe the microbiome and to identify potential factors that determine the structure of the microbial community, including the sex of the host, the impact of parasitoid infection, and the possible link between host plant and caterpillar microbiota. Our results demonstrate high variability of microbiota composition even among caterpillars that shared the same host plant individual. The observed variation in microbiota composition is partially attributed to the measured properties of the host or its plant microbial and chemical composition, and is aligned with microbial phylogenetic structure, with related taxa exhibiting similar patterns. However, the prevailing part of the observed variation was not associated with any of the assessed characteristics, although it followed a pronounced segregation structure: in some caterpillars the microbial communities were dominated by several related Enterobacteriaceae taxa, while in others these taxa were absent. Our results challenge previous findings that the host plant properties are the major drivers of microbiota communities of insect herbivores.

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CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

Microorganisms ◽

10.3390/microorganisms9040816 ◽

2021 ◽

Vol 9 (4) ◽

pp. 816

Author(s):

Matthew G. Links ◽

Tim J. Dumonceaux ◽

E. Luke McCarthy ◽

Sean M. Hemmingsen ◽

Edward Topp ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Dna Sequences ◽

Pcr Amplification ◽

Shotgun Sequencing ◽

Natural Ecosystems ◽

Gene Markers ◽

Microbial Profile ◽

Microbial Ecosystems ◽

Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

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PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

Journal of Animal Science ◽

10.1093/jas/skz258.594 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 293-294

Author(s):

Camila S Marcolla ◽

Benjamin Willing

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Relative Abundance ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Poultry Production ◽

Microbiota Composition ◽

Microbial Composition ◽

The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

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Establishment and maintenance of aphid endosymbionts after horizontal transfer is dependent on host genotype

Biology Letters ◽

10.1098/rsbl.2017.0016 ◽

2017 ◽

Vol 13 (5) ◽

pp. 20170016 ◽

Cited By ~ 12

Author(s):

Benjamin J. Parker ◽

Ailsa H. C. McLean ◽

Jan Hrček ◽

Nicole M. Gerardo ◽

H. Charles J. Godfray

Keyword(s):

Natural Selection ◽

Microbial Communities ◽

Host Plant ◽

Intraspecific Variation ◽

Horizontal Transfer ◽

Natural Populations ◽

Host Genotype ◽

Pea Aphids

Animal-associated microbial communities have important effects on host phenotypes. Individuals within and among species differ in the strains and species of microbes that they harbour, but how natural selection shapes the distribution and abundance of symbionts in natural populations is not well understood. Symbionts can be beneficial in certain environments but also impose costs on their hosts. Consequently, individuals that can or cannot associate with symbionts will be favoured under different ecological circumstances. As a result, we predict that individuals within a species vary in terms of how well they accept and maintain symbionts. In pea aphids, the frequency of endosymbionts varies among host-plant-associated populations (‘biotypes’). We show that aphid genotypes from different biotypes vary in how well they accept and maintain symbionts after horizontal transfer. We find that aphids from biotypes that frequently harbour symbionts are better able to associate with novel symbionts than those from biotypes that less frequently harbour symbionts. Intraspecific variation in the ability of hosts to interact with symbionts is an understudied factor explaining patterns of host–symbiont association.

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Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

10.21203/rs.3.rs-33130/v1 ◽

2020 ◽

Author(s):

Oskar Modin ◽

Raquel Liebana ◽

Soroush Saheb-Alam ◽

Britt-Marie Wilén ◽

Carolina Suarez ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Null Model ◽

Amplicon Sequencing ◽

Null Models ◽

Marker Genes ◽

Experimental Systems ◽

Microbial Community Assembly ◽

The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

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A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples

10.1101/2020.09.17.302836 ◽

2020 ◽

Author(s):

Federica Pinto ◽

Moreno Zolfo ◽

Francesco Beghini ◽

Federica Armanini ◽

Francesco Asnicar ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Microbial Community Composition ◽

Genetic Material ◽

Amplicon Sequencing ◽

Sample Type ◽

Natural Ecosystems ◽

Sediment Samples ◽

Water And Sediment ◽

Water And Sediment Samples

AbstractCultivation-free metagenomic analysis afforded unprecedented details on the diversity, structure and potential functions of microbial communities in different environments. When employed to study the viral fraction of the community that is recalcitrant to cultivation, metagenomics can shed light into the diversity of viruses and their role in natural ecosystems. However, despite the increasing interest in virome metagenomics, methodological issues still hinder the proper interpretation and comparison of results across studies. Virome enrichment experimental protocols are key multi-step processes needed for separating and concentrating the viral fraction from the whole microbial community prior to sequencing. However, there is little information on their efficiency and their potential biases. To fill this gap, we used metagenomic and amplicon sequencing to examine the microbial community composition through the serial filtration and concentration steps commonly used to produce viral-enriched metagenomes. The analyses were performed on water and sediment samples from an Alpine lake. We found that, although the diversity of the retained microbial communities declined progressively during the serial filtration, the final viral fraction contained a large proportion (from 10% to 40%) of non-viral taxa, and that the efficacy of filtration showed biases based on taxonomy. Our results quantified the amount of bacterial genetic material in viromes and highlighted the influence of sample type on the enrichment efficacy. Moreover, since viral-enriched samples contained a significant portion of microbial taxa, computational sequence analysis should account for such biases in the downstream interpretation pipeline.ImportanceFiltration is a commonly used method to enrich viral particles in environmental samples. However, there is little information on its efficiency and potential biases on the final result. Using a sequence-based analysis on water and sediment samples, we found that filtration efficacy is dependent on sample type and that the final virome contained a large proportion of non-viral taxa. Our finding stressed the importance of downstream analysis to avoid biased interpretation of data.

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A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure

Molecules ◽

10.3390/molecules26237332 ◽

2021 ◽

Vol 26 (23) ◽

pp. 7332

Author(s):

Miguel David Marfil-Santana ◽

Anahí Martínez-Cárdenas ◽

Analuisa Ruíz-Hernández ◽

Mario Vidal-Torres ◽

Norma Angélica Márquez-Velázquez ◽

...

Keyword(s):

Microbial Community ◽

Secondary Metabolites ◽

Microbial Communities ◽

Secondary Metabolite ◽

Resistant Bacteria ◽

Mangrove Sediments ◽

Molecular Networking ◽

Mangrove Tree ◽

Enhanced Production ◽

The Impact

Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.

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Spatiotemporal Correlations Between Water Quality And Microbial Community of Typical Inflow River Into Taihu Lake, China

10.21203/rs.3.rs-1000115/v1 ◽

2021 ◽

Author(s):

Yajie Zhang ◽

Ye Zhang ◽

Lecheng Wei ◽

Mengyan Li ◽

Weitang Zhu ◽

...

Keyword(s):

Water Quality ◽

Microbial Community ◽

Microbial Communities ◽

Taihu Lake ◽

Wastewater Treatment Plants ◽

Ammonia Nitrogen ◽

Pollution Sources ◽

Storm Water ◽

Urban Wastewater Treatment ◽

The Impact

Abstract Changxing River, which is a typical inflow river into the Taihu Lake and occurs severe algae invasion, is selected to study the effect of different pollution sources on the water quality and ecological system. Four types of pollution sources, including the estuary of Taihu Lake, discharge outlets of urban wastewater treatment plants, storm water outlets, and non-point source agricultural drainage areas are chosen, and next-generation sequencing and multi-variate statistical analyses are used to characterize the microbial communities and reveal their relationship with water physicochemical properties. Results showed that ammonia nitrogen (NH4+-N), total nitrogen (TN), and total phosphorus (TP) are the main pollutant in Changxing River, especially at storm water outlets. At the same time, the diversity of microbial communities was the highest in the summer, and dominant phyla included Proteobacteria (40.9%), Bacteroidetes (21.0%) and Euryarchaeota (6.1%) under the condition of algal bloom. Water temperature (T), air pressure (P), concentrations of TP and CODMn were the important variables for the succession of microbial community. From the perspective of different pollution types, relative abundances of Microcystis and Nostocaceae at the estuary of Taihu Lake were correlated positively with dissolved oxygen (DO) and pH, and Pseudomonas and Arcobacter were correlated positively with concentrations of TN and nitrate nitrogen (NO3--N) at storm water outlets. The results provide a reference for the impact of pollution types on river microbial ecosystem under complex hydrological condition and a guidance for the selection of restoration techniques for polluted rivers entering an important lake.

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Heavy Metal Tolerance Genes Associated With Contaminated Sediments From an E-Waste Recycling River in Southern China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.665090 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shengqiao Long ◽

Hui Tong ◽

Xuxiang Zhang ◽

Shuyu Jia ◽

Manjia Chen ◽

...

Keyword(s):

Heavy Metal ◽

Microbial Community ◽

Microbial Communities ◽

Southern China ◽

Risk Index ◽

River Sediments ◽

Microbial Community Composition ◽

Heavy Metal Tolerance ◽

Waste Recycling ◽

The Impact

Heavy metal pollution that results from electronic waste (e-waste) recycling activities has severe ecological environmental toxicity impacts on recycling areas. The distribution of heavy metals and the impact on the bacteria in these areas have received much attention. However, the diversity and composition of the microbial communities and the characteristics of heavy metal resistance genes (HMRGs) in the river sediments after long-term e-waste contamination still remain unclear. In this study, eight river sediment samples along a river in a recycling area were studied for the heavy metal concentration and the microbial community composition. The microbial community consisted of 13 phyla including Firmicutes (ranging from 10.45 to 36.63%), Proteobacteria (11.76 to 32.59%), Actinobacteria (14.81 to 27.45%), and unclassified bacteria. The abundance of Firmicutes increased along with the level of contaminants, while Actinobacteria decreased. A canonical correspondence analysis (CCA) showed that the concentration of mercury was significantly correlated with the microbial community and species distribution, which agreed with an analysis of the potential ecological risk index. Moreover, manually curated HMRGs were established, and the HMRG analysis results according to Illumina high-throughput sequencing showed that the abundance of HMRGs was positively related to the level of contamination, demonstrating a variety of resistance mechanisms to adapt, accommodate, and live under heavy metal-contaminated conditions. These findings increase the understanding of the changes in microbial communities in e-waste recycling areas and extend our knowledge of the HMRGs involved in the recovery of the ecological environment.

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Phytoremediation of landfill leachate in constructed wetland

Linnaeus Eco-Tech ◽

10.15626/eco-tech.2005.046 ◽

2019 ◽

pp. 441-446

Author(s):

Jaak Truu ◽

Jaanis Juhanson ◽

Mait Kriipsalu ◽

Marit Seene

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Plant Species ◽

Landfill Leachate ◽

Water Samples ◽

Free Water ◽

Vegetation Period ◽

Quality Of Water ◽

Remediation Plan ◽

The Impact

The integrated remediation plan of the Laguja landfill, Estonia, includes creation of aconstructed wetland for treatment of landfill leachate. A mesocosm experiment wasconducted in order to estimate the impact of different plant species on purification efficiencyof wetland. The quality of water in mesocosms was monitored during vegetation period. Allplant treatments enhanced reduction of organic matter (BOD: 87-96%, COD: ca 30%, TOC:ca 50%) as well as ammonia and total nitrogen in water compared to unplanted control.Presence of plants enhanced biodegradative bacterial abundance and activity as well asmetabolic diversity of microbial community in water. Water samples from all plant treatmentswere characterized by distinct microbial communities as revealed by molecular fingerprintingtechniques. Most different from the rest of microbial communities were water samples frommesocosm with plants on floating mats. Our results show that in free-water constructedwetlands with vegetation the purification efficiency is not dependent on plant species, whilestructure of water microbial community differs due to plant species.

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A coexistence theory in microbial communities

Royal Society Open Science ◽

10.1098/rsos.180476 ◽

2018 ◽

Vol 5 (9) ◽

pp. 180476 ◽

Cited By ~ 4

Author(s):

Marina Dohi ◽

Akihiko Mougi

Keyword(s):

Microbial Community ◽

Equilibrium State ◽

Microbial Communities ◽

Critical Role ◽

Abundance Ratio ◽

The Other ◽

Natural Ecosystems ◽

Trade Off ◽

Coexistence Theory ◽

Different Types

Microbes are widespread in natural ecosystems where they create complex communities. Understanding the functions and dynamics of such microbial communities is a very important theme not only for ecology but also for humankind because microbes can play major roles in our health. Yet, it remains unclear how such complex ecosystems are maintained. Here, we present a simple theory on the dynamics of a microbial community. Bacteria preferring a particular pH in their environment indirectly inhibit the growth of the other types of bacteria by changing the pH to their optimum value. This pH-driven interaction always causes a state of bistability involving different types of bacteria that can be more or less abundant. Furthermore, a moderate abundance ratio of different types of bacteria can confer enhanced resilience to a specific equilibrium state, particularly when a trade-off relationship exists between growth and the ability of bacteria to change the pH of their environment. These results suggest that the balance of the composition of microbiota plays a critical role in maintaining microbial communities.

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