scholarly journals Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Mimiviridae, and prokaryotes in a coastal ecosystem

2021 ◽  
Author(s):  
Florian Prodinger ◽  
Hisashi Endo ◽  
Yoshihito Takano ◽  
Yanze Li ◽  
Kento Tominaga ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Dynamics ◽  
Environmental Changes ◽  
Interspecific Interactions ◽  
Survival Strategies ◽  
Marker Genes ◽  
Sequence Variant ◽  
Dna Viruses ◽  
Seawater Samples ◽  
One Year

AbstractCoastal seawater is the habitat of different microbial communities. These communities are affected by seasonal environmental changes and fluctuating nutrient availability, as well as competitive and cooperative interspecific interactions. In this work, we investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses infecting eukaryotes (i.e. Mimiviridae), as well as prokaryotes in the Uranouchi Inlet, Kochi, Japan. We performed metabarcoding using ribosomal RNA genes and the Mimiviridae polB gene as marker genes in 43 seawater samples collected during 20 months. Communities characterized by the compositions of amplicon sequence variants (ASVs) showed synchronic seasonal cycles for eukaryotes, Mimiviridae, and prokaryotes. However, the community dynamics showed intriguing differences in several aspects such as the recovery rate after a year. We further show that the differences in the community dynamics can be explained by differences in the recurrence/persistence levels of individual ASVs among eukaryotes, Mimiviridae, and prokaryotes. Mimiviridae ASVs were less persistent than eukaryotic ASVs, and prokaryotic ASVs were the most persistent. We argue that the differences in the specificity of interactions (i.e. virus-eukaryote vs prokaryote-eukaryote) as well as the survival strategies are at the origin of the distinct community dynamics among eukaryotes, Mimiviridae, and prokaryotes.One sentence summaryA one year observation of coastal microbial communities revealed similar but different community dynamics for eukaryotes, a group of large viruses, and prokaryotes.

scholarly journals Role of phylogenetic structure in the dynamics of coastal viral assemblages

2021 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Curtis A. Suttle
Keyword(s):  
High Throughput Sequencing ◽  
Environmental Changes ◽  
Marine Ecosystem ◽  
Marker Genes ◽  
Marine Microbes ◽  
Phylogenetic Structure ◽  
Genes Encoding ◽  
One Year ◽  
Rna And Dna

Marine microbes, including viruses, are an essential part of the marine ecosystem, forming the base of the foodweb and driving biogeochemical cycles. Within this system, the composition of viral assemblages changes markedly with time, with some of these changes being repeatable through time; however, the extent to which these dynamics are reflected within versus among evolutionarily-related groups of viruses is largely unexplored. To examine these dynamics, changes in the composition of two groups of ecologically important viruses and communities of their potential hosts were sampled every two weeks for 13 months at a coastal site in British Columbia, Canada. We sequenced two marker genes for viruses, the major capsid protein (gp23) of T4-like phages and their relatives, and the RNA-dependent RNA polymerase (RdRp) of marnavirus-like RNA viruses, as well as their bacterial and eukaryotic host communities, the genes encoding 16S and 18S ribosomal RNA (rRNA). There were strong lagged correlations between viral diversity and community similarity of putative hosts implying that the viruses influenced the composition of the host communities. The results showed that for both viral assemblages, the dominant clusters of phylogenetically-related viruses shifted over time and this was correlated with environmental changes. Viral clusters contained many ephemeral taxa and few persistent taxa, but within a viral assemblage the ephemeral and persistent taxa were closely related implying ecological dynamics within these clusters. Furthermore, these dynamics occurred in both the RNA and DNA viral assemblages surveyed, implying that this structure is common in natural viral assemblages. Importance Viruses are major agents of microbial mortality in marine systems; yet, little is known about changes in the composition of viral assemblages in relation to that of the microbial communities that they infect. Here, we sampled coastal seawater every two weeks for one year and used high-throughput sequencing of marker genes to follow changes in the composition of two groups of ecologically important viruses, as well as the communities of bacteria and protists that serve as their respective hosts. Different subsets of genetically related viruses dominated at different times. These results demonstrate that although the genetic composition of viral genotypes is highly dynamic temporally, for the most part the shuffling of genotypes occurs within a few clusters of phylogenetically related viruses. Thus, it appears that even in temperate coastal waters with large seasonal changes the highly dynamic shuffling of viral genotypes largely occurs within a few subsets of related individuals.

Effects of Community Versus Single Strain Inoculants on the Biocontrol of Salmonella and Microbial Community Dynamics in Alfalfa Sprouts†

2005 ◽  
Vol 68 (1) ◽  
pp. 40-48 ◽  
Author(s):  
ANABELLE MATOS ◽  
JAY L. GARLAND
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Community Level ◽  
Microbial Consortia ◽  
Single Strain ◽  
Acridine Orange Staining ◽  
Physiological Profiles ◽  
Alfalfa Sprouts ◽  
Alfalfa Seeds

Potential biological control inoculants, Pseudomonas fluorescens 2-79 and microbial communities derived from market sprouts or laboratory-grown alfalfa sprouts, were introduced into alfalfa seeds with and without a Salmonella inoculum. We examined their ability to inhibit the growth of this foodborne pathogen and assess the relative effects of the inoculants on the alfalfa microbial community structure and function. Alfalfa seeds contaminated with a Salmonella cocktail were soaked for 2 h in bacterial suspensions from each inoculant tested. Inoculated alfalfa seeds were grown for 7 days and sampled during days 1, 3, and 7. At each sampling, alfalfa sprouts were sonicated for 7 min to recover microflora from the surface, and the resulting suspensions were diluted and plated on selective and nonselective media. Total bacterial counts were obtained using acridine orange staining, and the percentage culturability was calculated. Phenotypic potential of sprout-associated microbial communities inoculated with biocontrol treatments was assessed using community-level physiological profiles based on patterns of use of 95 separate carbon sources in Biolog plates. Community-level physiological profiles were also determined using oxygen-sensitive fluorophore in BD microtiter plates to examine functional patterns in these communities. No significant differences in total and mesophilic aerobe microbial cell density or microbial richness resulting from the introduction of inoculants on alfalfa seeds with and without Salmonella were observed. P. fluorescens 2-79 exhibited the greatest reduction in the growth of Salmonella early during alfalfa growth (4.22 log at day 1), while the market sprout inoculum had the reverse effect, resulting in a maximum log reduction (5.48) of Salmonella on day 7. Community-level physiological profiles analyses revealed that market sprout communities peaked higher and faster compared with the other inoculants tested. These results suggest that different modes of actions of single versus microbial consortia biocontrol treatments may be involved.

scholarly journals Effects of Lime Application and Understory Removal on Soil Microbial Communities in Subtropical Eucalyptus L’Hér. Plantations

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 338 ◽  
Author(s):  
Songze Wan ◽  
Zhanfeng Liu ◽  
Yuanqi Chen ◽  
Jie Zhao ◽  
Qin Ying ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Litter Decomposition ◽  
Decomposition Rate ◽  
Environmental Changes ◽  
Soil Microbial Communities ◽  
Dissolved Carbon ◽  
Soil Microbial ◽  
Litter Decomposition Rate ◽  
Eucalyptus Plantations ◽  
Lime Application

Soil microorganisms play key roles in ecosystems and respond quickly to environmental changes. Liming and/or understory removal are important forest management practices and have been widely applied to planted forests in humid subtropical and tropical regions of the world. However, few studies have explored the impacts of lime application, understory removal, and their interactive effects on soil microbial communities. We conducted a lime application experiment combined with understory removal in a subtropical Eucalyptus L’Hér. plantation. Responses of soil microbial communities (indicated by phospholipid fatty acids, PLFAs), soil physico-chemical properties, and litter decomposition rate to lime and/or understory removal were measured. Lime application significantly decreased both fungal and bacterial PLFAs, causing declines in total PLFAs. Understory removal reduced the fungal PLFAs but had no effect on the bacterial PLFAs, leading to decreases in the total PLFAs and in the ratio of fungal to bacterial PLFAs. No interaction between lime application and understory removal on soil microbial community compositions was observed. Changes in soil microbial communities caused by lime application were mainly attributed to increases in soil pH and NO3–-N contents, while changes caused by understory removal were mainly due to the indirect effects on soil microclimate and the decreased soil dissolved carbon contents. Furthermore, both lime application and understory removal significantly reduced the litter decomposition rates, which indicates the lime application and understory removal may impact the microbe-mediated soil ecological process. Our results suggest that lime application may not be suitable for the management of subtropical Eucalyptus plantations. Likewise, understory vegetation helps to maintain soil microbial communities and litter decomposition rate; it should not be removed from Eucalyptus plantations.

scholarly journals Changes in Soil Arthropod Abundance and Community Structure across a Poplar Plantation Chronosequence in Reclaimed Coastal Saline Soil

Forests ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 644 ◽  
Author(s):  
Yuanyuan Li ◽  
Han Chen ◽  
Qianyun Song ◽  
Jiahui Liao ◽  
Ziqian Xu ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Stand Age ◽  
Stand Development ◽  
Soil Arthropods ◽  
Total Abundance ◽  
Soil Arthropod ◽  
Plantation Development ◽  
Poplar Plantations ◽  
Hill Numbers ◽  
One Year

Poplar plantations have the capacity to improve the properties of soils in muddy coastal areas; however, our understanding of the impacts of plantation development on soil arthropods remains limited. For this study, we determined the community dynamics of soil dwelling arthropods across poplar plantations of different ages (5-, 10-, and 21-years) over the course of one year in Eastern Coastal China. The total abundance of soil arthropods differed with stand development. Further, there were some interactions that involved the sampling date. On average, total abundance was highest in the 10-year-old stands and lowest in the 5-year-old stands. Total abundance exhibited strong age-dependent trends in June and September, but not in March or December. The abundance of Prostigmata and Oribatida increased in the 5- to 21-year-old stands, with the highest levels being in the 10-year-old stands. The abundance of Collembola increased with stand development; however, the stand age had no significant impact on the abundance of epedapic, hemiedaphic, and euedaphic Collembola. Order richness (Hill number q = 0) curve confidence intervals overlapped among three stand ages. Shannon and Simpson diversity (Hill numbers q = 1 and q = 2) differed between 10- and 21-year-old stand age. They showed almost similar trends, and the highest and lowest values were recorded in the 21- and 10-year-old stand ages, respectively. Permutational multivariate analysis of variance demonstrated that composition also varied significantly with the sampling date and stand age, and the 10-year-old stands that were sampled in June stood well-separated from the others. Indicator analysis revealed that Scolopendromorpha and Prostigmata were indicators in June for the 10-year-old stands, while Collembola were indicators for the 21-year-old stands sampled in September. Our results highlight that both stand development and climate seasonality can significantly impact soil arthropod community dynamics in the reclaimed coastal saline soils of managed poplar plantations.

scholarly journals A network-based approach to deciphering a dynamic microbiome’s response to a subtle perturbation

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Grace Tzun-Wen Shaw ◽  
An-Chi Liu ◽  
Chieh-Yin Weng ◽  
Yi-Chun Chen ◽  
Cheng-Yu Chen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Ecosystem Functioning ◽  
Environmental Changes ◽  
Ecosystem Dynamics ◽  
Environmental Research ◽  
Human Society ◽  
The Past ◽  
Environmental Perturbations ◽  
Before And After ◽  
Occurrence Patterns

Abstract Over the past decades, one main issue that has emerged in ecological and environmental research is how losses in biodiversity influence ecosystem dynamics and functioning, and consequently human society. Although biodiversity is a common indicator of ecosystem functioning, it is difficult to measure biodiversity in microbial communities exposed to subtle or chronic environmental perturbations. Consequently, there is a need for alternative bioindicators to detect, measure, and monitor gradual changes in microbial communities against these slight, chronic, and continuous perturbations. In this study, microbial networks before and after subtle perturbations by adding S. acidaminiphila showed diverse topological niches and 4-node motifs in which microbes with co-occurrence patterns played the central roles in regulating and adjusting the intertwined relationships among microorganisms in response to the subtle environmental changes. This study demonstrates that microbial networks are a good bioindicator for chronic perturbation and should be applied in a variety of ecological investigations.

scholarly journals MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 726
Author(s):  
Mike W.C. Thang ◽  
Xin-Yi Chua ◽  
Gareth Price ◽  
Dominique Gorse ◽  
Matt A. Field
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Metagenomic Data ◽  
Marker Genes ◽  
Metagenomic Sequencing ◽  
Differential Analysis ◽  
Biomedical Sciences ◽  
Metagenomic Sequence ◽  
Differential Abundance ◽  
Differential Abundance Analysis

Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences.  While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs.  Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics.  MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

scholarly journals Links between mouse and vole social networks and their gut microbiomes support predictions from metacommunity theory

2020 ◽  
Author(s):  
Joël W. Jameson ◽  
Steven W. Kembel ◽  
Denis Réale
Keyword(s):  
Social Networks ◽  
Host Species ◽  
Community Dynamics ◽  
Peromyscus Maniculatus ◽  
Interspecific Interactions ◽  
Host Community ◽  
Social Proximity ◽  
Strongly Connected ◽  
Bacterial Transmission

ABSTRACTMetacommunity theory predicts that strongly connected individuals will harbour similar gut microbiomes (GMs) and affiliating with more individuals should increase GM diversity. Additionally, cross-species bacterial transmission may play a role in how interspecific interactions affect host community dynamics. We tracked sympatric mice (Peromyscus maniculatus) and voles (Myodes gapperi) and constructed social networks for each species and both species together. We tested whether: 1) similarity in GM composition between individuals correlates with their social proximity within and across species; 2) GM diversity correlates with a host’s number of conspecific or heterospecific neighbours. We could not differentiate associations between GM composition and mouse social proximity or habitat. In voles, social proximity explained part of the GM composition. GM composition associated with interspecific social proximity, and mouse GM diversity correlated with number of vole neighbours. Contributions of host-host bacterial transmission to the GM partly follow metacommunity theory but depend on host species.

scholarly journals Zooplankton community dynamics and environmental factors in Lake Ozeros (Greece)

2013 ◽  
Vol 14 (3) ◽  
pp. 32 ◽  
Author(s):  
E. CHALKIA ◽  
G. KEHAYIAS
Keyword(s):  
Community Dynamics ◽  
Zooplankton Community ◽  
Trophic State Index ◽  
Zooplankton Abundance ◽  
The Novel ◽  
Effective Management ◽  
Eutrophic Lakes ◽  
State Index ◽  
The Mean ◽  
One Year

A one year investigation of the zooplankton community composition and dynamics in Lake Οzeros (western Greece) revealed 25 invertebrate species (16 rotifers, three copepods, five cladocerans and one mollusc larva). The mean zooplankton abundance fluctuated between 59.4 to 818 ind l-1, having maximum values in spring. The species composition and seasonal variation do not differentiate Lake Ozeros from the nearby lakes. The presence of the dominant calanoid copepod Eudiaptomus drieschi and some of the rotifer species recorded are characteristics of either oligo- or eutrophic lakes. According to the trophic state index (TSI) Lake Ozeros is a meso-eutrophic ecosystem, in which the eutrophic character was possibly the result of the high charge with phosphorus (being raised by 28.9 % in comparison to previous decades), which came into the lake via the surrounding agricultural cultivations and mainly the pig-raising activities. In contrast, the concentrations of ΝΟ3, ΝΟ2 and NH4 have considerably decreased possibly due to the termination of the tobacco cultivations around the lake during the last years. The novel information on the abiotic and especially the biotic elements of Lake Ozeros provided by the present study can contribute to the effective management of this aquatic ecosystem in the future.

scholarly journals Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes

2018 ◽  
Author(s):  
Oswaldo C Villena ◽  
Bahram Momen ◽  
Joseph Sullivan ◽  
Paul T Leisnham
Keyword(s):  
Metabolic Rate ◽  
Microbial Communities ◽  
Aedes Albopictus ◽  
Culex Pipiens ◽  
Environmental Changes ◽  
Negative Impact ◽  
Transmission Rate ◽  
Major Effect ◽  
Control Group ◽  
Metabolic Rates

Environmental changes will alter many environmental factors in the coming years including temperature, precipitation, humidity, and the amount of solar radiation reaching the earth’s surface, which in turn will have an impact on living organisms like invertebrates. In this study, we assessed the effect of UV-B radiation upon the metabolic rate and upon three fitness parameters (survival, development time, and body size) of the mosquitoes Aedes albopictus and Culex pipiens, and upon the production of microbial resources on which mosquito larvae feed in aquatic microcosms. We set up three UV-B radiation treatments mimicking levels typically measured in full-sun (FS) and shade (S) conditions, as well as a control group with no UV-B radiation (NUV). The metabolic rate expressed as heat production (µwatts/ml) for larvae and microbial community was measured at days 1, 8, and 15. Our results indicated that UV-B radiation affected the metabolic rate of both Cx. pipiens and Ae. albopictus larvae; metabolic rates were significantly higher in full-sun (FS) compared to shade (S) and no-UV condition (NUV), at days 8 and 15 compared to day 1 (Figures 1A and 1B). Culex pipiens metabolic rates were significantly higher than Ae. albopictus at day 15 compared to days 1 and 8 (Figure 1B). Metabolic rates were significantly lower in microbial communities from vials with Ae. albopictus larvae, Cx. pipiens larvae, and no larvae in FS conditions compared to vials from S and NUV conditions, especially at day 8 (Figure 2A and 2B). There was a major effect of UV-B conditions only on the survival of Ae. albopictus and Cx. pipiens mosquitoes, with significantly lower survival in FS compared to S and NUV conditions. UV-B radiation at levels found in aquatic environments in open fields showed a negative impact on the metabolic rate of Ae. albopictus and Cx. pipiens larvae and on the microbial communities on which they feed. These negative impacts could have important implications for the distribution and abundance of these mosquitoes and for the transmission rate of illness caused by the pathogens that these two broadly distributed mosquitoes transmit.

Sign in / Sign up

Export Citation Format

Share Document