Effect of ambient water conditions on microbial communities on the artificially produced aggregates: Evidence from experiments using two different seawater cultures

2021 ◽  
Author(s):  
Markus Weinbauer ◽  
Chiaki Motegi ◽  
Christophe Migon ◽  
Xavier Mari
Keyword(s):  
Microbial Communities ◽  
Water Flow ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Ambient Water ◽  
Lagoon Water ◽  
Water Conditions ◽  
Flow Experiment ◽  
Water Treatments

<p>Microbial communities on marine aggregates could be influenced by ambient water conditions; however, empirical data are scarce. In this study, we used fingerprint analysis of PCR-amplified 16S rRNA gene fragment to examine how microbial communities on aggregates change in response to different conditions of ambient water. We conducted two experiments using seawater cultures from surface waters of the lagoon and the anthropogenically influenced bay of Nouméa, New Caledonia: a transplant experiment in which the artificially produced aggregates from one station was added to ultra-filtered seawater culture of another station, and a water-flow experiment in which the artificially produced aggregates placed in the ultra-filtered seawater culture with or without water-flow. In a transplant experiment, bacterial community composition (BCC) on the bay and lagoon water aggregates were significantly different (<em>p < 0.05</em>, ANOSIM) at the beginning of experiment. After 11 days of incubation, BCC on the lagoon water aggregates were significantly different (<em>p < 0.05</em>) from transplanted communities. Transplantation effect was also observed in the bay water treatments. In a water-flow experiment, BCC on the bay and lagoon water aggregates were significantly different (<em>p < 0.05</em>) at the beginning of the experiment. BCC on the lagoon and bay water aggregates with and without water-flow treatments were significantly different (<em>p </em>< 0.05) at the end of incubation, and effect of water-flow on BCC were observed in the bay and lagoon water treatments. Our experimental studies suggest that changes in ambient water conditions potentially influence microbial communities on aggregates in the Bay of Nouméa.</p>

scholarly journals Effects of Wildfire and Harvest Disturbances on Forest Soil Bacterial Communities

2007 ◽  
Vol 74 (1) ◽  
pp. 216-224 ◽  
Author(s):  
Nancy R. Smith ◽  
Barbara E. Kishchuk ◽  
William W. Mohn
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Biomass Carbon ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Microbial Biomass Nitrogen ◽  
Soil Microbial

ABSTRACT Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH4 + and NO3 − due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma- and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.

scholarly journals Locally Adapted Mimulus Ecotypes Differentially Impact Rhizosphere Bacterial and Archaeal Communities in an Environment-Dependent Manner

2020 ◽  
Vol 4 (1) ◽  
pp. 53-63 ◽  
Author(s):  
Alan W. Bowsher ◽  
Patrick J. Kearns ◽  
Damian Popovic ◽  
David B. Lowry ◽  
Ashley Shade
Keyword(s):  
Microbial Communities ◽  
Plant Root ◽  
Alpha Diversity ◽  
Local Environment ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Dependent Manner ◽  
Reciprocal Transplant Experiment ◽  
Soil Microbial Community Structure ◽  
Host Identity

Plant root−microbe interactions influence plant productivity, health, and resistance to stress. Although there is evidence that plant species and even genotypes can alter soil microbial community structure, environmental conditions can potentially outweigh plant genetic effects. Here, we used a reciprocal transplant experiment to understand the contributions of the environment and the host plant to rhizosphere microbiome composition in locally adapted ecotypes of Mimulus guttatus (syn. Erythranthe guttata). Two genotypes of a coastal ecotype and two genotypes of an inland ecotype were planted at coastal and inland sites. After 3 months, we collected rhizosphere and bulk soil and assessed microbial communities by 16S rRNA gene sequencing. We found that local environment (coastal versus inland site) strongly influenced rhizosphere communities, at least in part due to distinct local microbial species pools. Host identity played a smaller role: at each site, the ecotypes exhibited remarkably similar composition of microbial communities at the class level, indicating that divergent M. guttatus ecotypes recruit phylogenetically similar rhizosphere communities, even in environments to which they are maladapted. Nevertheless, the two ecotypes significantly differed in community composition at both sites due, in part, to an exclusive set of taxa associated with each ecotype. They also differed in alpha diversity at the inland site. Although this indicates that locally adapted M. guttatus ecotypes are genetically diverged in factors shaping rhizosphere communities, our findings highlight the context-specific interactions between host identity and local environment that shape those communities. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Biogeographical distribution of Microbial Communities along the Rajang River-South China Sea Continuum

2019 ◽  
Author(s):  
Edwin Sien Aun Sia ◽  
Zhuoyi Zhu ◽  
Jing Zhang ◽  
Wee Cheah ◽  
Jiang Shan ◽  
...  
Keyword(s):  
South China Sea ◽  
Microbial Communities ◽  
Community Composition ◽  
South China ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Drainage System ◽  
Rrna Gene ◽  
China Sea ◽  
Biogeographical Distribution

Abstract. Microbial community composition and diversity in freshwater habitats, especially in lotic environments, are much less studied compared to marine and soil communities. The Rajang River is the main drainage system for central Sarawak in Malaysian Borneo and passes through peat domes whereby peat-rich material is being fed into the system and eventually into the southern South China Sea. Microbial communities found within peat-rich systems are important biogeochemical cyclers in terms of methane and carbon dioxide sequestration. To address the critical lack of knowledge about microbial communities in tropical (peat-draining) rivers, this study represents the first seasonal assessment targeted at establishing a foundational understanding of the microbial communities of the Rajang River-South China Sea continuum. This was carried out utilizing 16S rRNA gene amplicon sequencing via Illumina MiSeq in size-fractionated samples (0.2 and 3.0 μm GF/C filter membranes) covering different biogeographical features/sources from headwaters to coastal waters. The microbial communities found along the Rajang river exhibited taxa common to rivers (i.e. the predominance of β-Proteobacteria) while estuarine and marine regions exhibited taxa that were common to the aforementioned regions as well (i.e. predominance of α- and γ-Proteobacteria). This is in agreement with studies from other rivers which observed similar changes along the salinity gradients. In terms of particulate versus free-living bacteria, nonmetric multi-dimensional scaling (NMDS) results showed similarly distributed microbial communities with varying separation between seasons. Distinct patterns were observed based on linear models as a result of the changes in salinity along with variation of other biogeochemical parameters. Alpha diversity indices indicated that microbial communities were higher in diversity upstream compared to the marine and estuarine regions whereas anthropogenic perturbations led to increased richness but less diversity. Despite the observed changes in bacterial community composition and diversity that occur along the Rajang River to sea continuum, the PICRUST predictions showed minor variations. The results provide essential context for future studies such as further analyses on the ecosystem health in response to anthropogenic land-use practices and probable development of biomarkers to improve the monitoring of water quality in this region.

scholarly journals Short-term exposure to benzalkonium chloride in bacteria from activated sludge alters the community diversity and the antibiotic resistance profile

2021 ◽  
Author(s):  
Luz Chacón ◽  
Maria Arias-Andres ◽  
Freylan Mena ◽  
Luis Rivera ◽  
Lorena Hernández ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Activated Sludge ◽  
Microbial Communities ◽  
Benzalkonium Chloride ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Community Diversity ◽  
Rrna Gene ◽  
Short Term Exposure

Abstract The continuous introduction of cleaning products containing benzalkonium chloride (BAC) from household discharges can mold the microbial communities in wastewater treatment plants (WWTPs) in a way still poorly understood. In this study, we performed an in vitro exposure of activated sludge from a WWTP in Costa Rica to BAC, quantified the changes in intI1, sul2, and qacE/qacEΔ1 gene profiles, and determined alterations in the bacterial community composition. The analysis of the qPCR data revealed elevated charges of antibiotic resistance genes in the microbial community; after BAC's exposure, a significant increase in the qacE/qacEΔ1 gene, which is related to ammonium quaternary resistance, was observed. The 16S rRNA gene sequences’ analysis showed pronounced variations in the structure of the bacterial communities, including reduction of the alpha diversity values and an increase of the relative abundance of Alphaproteobacteria, particularly of Rhodospseudomonas and Rhodobacter. We confirmed that the microbial communities presented high resilience to BAC at the mg/mL concentration, probably due to constant exposure to this pollutant. They also presented antibiotic resistance-related genes with similar mechanisms to tolerate this substance. These mechanisms should be explored more thoroughly, especially in the context of high use of disinfectant.

scholarly journals Biogeographical distribution of microbial communities along the Rajang River–South China Sea continuum

2019 ◽  
Vol 16 (21) ◽  
pp. 4243-4260
Author(s):  
Edwin Sien Aun Sia ◽  
Zhuoyi Zhu ◽  
Jing Zhang ◽  
Wee Cheah ◽  
Shan Jiang ◽  
...  
Keyword(s):  
South China Sea ◽  
Microbial Communities ◽  
South China ◽  
Linear Models ◽  
Bacterial Community Composition ◽  
Drainage System ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
China Sea ◽  
Biogeographical Distribution

Abstract. The Rajang River is the main drainage system for central Sarawak in Malaysian Borneo and passes through peat domes through which peat-rich material is being fed into the system and eventually into the southern South China Sea. Microbial communities found within peat-rich systems are important biogeochemical cyclers in terms of methane and carbon dioxide sequestration. To address the critical lack of knowledge about microbial communities in tropical (peat-draining) rivers, this study represents the first seasonal assessment targeted at establishing a foundational understanding of the microbial communities of the Rajang River–South China Sea continuum. This was carried out utilising 16S rRNA gene amplicon sequencing via Illumina MiSeq in size-fractionated samples (0.2 and 3.0 µm GF/C filter membranes) covering different biogeographical features and sources from headwaters to coastal waters. The microbial communities found along the Rajang River exhibited taxa common to rivers (i.e. predominance of β-Proteobacteria) while estuarine and marine regions exhibited taxa that were common to the aforementioned regions as well (i.e. predominance of α− and γ-Proteobacteria). This is in agreement with studies from other rivers which observed similar changes along salinity gradients. In terms of particulate versus free-living bacteria, nonmetric multi-dimensional scaling (NMDS) results showed similarly distributed microbial communities with varying separation between seasons. Distinct patterns were observed based on linear models as a result of the changes in salinity along with variation of other biogeochemical parameters. Alpha diversity indices indicated that microbial communities were higher in diversity upstream compared to the marine and estuarine regions, whereas anthropogenic perturbations led to increased richness but less diversity. Despite the observed changes in bacterial community composition and diversity that occur along the continuum of the Rajang River to the sea, the PICRUSt predictions showed minor variations. The results provide essential context for future studies such as further analyses on the ecosystem response to anthropogenic land-use practices and probable development of biomarkers to improve the monitoring of water quality in this region.

scholarly journals Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds

2020 ◽  
Vol 8 (2) ◽  
pp. 311
Author(s):  
Xin Tai ◽  
Rui Li ◽  
Bao Zhang ◽  
Hao Yu ◽  
Xiao Kong ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Community Assembly ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Sediment Samples ◽  
Pollution Levels ◽  
Water And Sediment

Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the succession of microbial communities in different pollution levels rural ponds. Also, the processes that govern bacterial communities in polluted ponds are poorly understood. In this study, the microbial communities in water and sediment from the ponds were investigated by using the 16S rRNA gene high-throughput sequencing technology. Meanwhile, we used null model analyses based on a taxonomic and phylogenetic metrics approach to test the microbial community assembly processes. Pollution levels were found to significantly alter the community composition and diversity of bacteria. In the sediment samples, the bacterial diversity indices decreased with increasing pollutant levels. Between-community analysis revealed that community assembly processes among water and sediment samples stochastic ratio both gradually decreased with the increased pollution levels, indicating a potential deterministic environmental filtering that is elicited by pollution. Our results identified assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for contaminated freshwater systems.

scholarly journals Locally-adapted Mimulus ecotypes differentially impact rhizosphere bacterial and archaeal communities in an environment-dependent manner

2019 ◽  
Author(s):  
Alan W. Bowsher ◽  
Patrick J. Kearns ◽  
Damian Popovic ◽  
David B. Lowry ◽  
Ashley Shade
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Plant Root ◽  
16S Rrna Gene Sequencing ◽  
Wild Plants ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Dependent Manner ◽  
Reciprocal Transplant Experiment ◽  
Soil Microbial Community Structure

AbstractPlant root-microbe interactions influence plant productivity, health, and resistance to stress. Although there is evidence that plant species and even genotypes can alter soil microbial community structure, environmental conditions can potentially outweigh plant genetic effects. Here, we used a reciprocal transplant experiment to understand the contributions of the environment and the host plant to rhizosphere microbiome composition in locally-adapted ecotypes of Mimulus guttatus (syn. Erythranthe guttata (Fisch. ex DC.) G.L. Nesom). Two genotypes of a coastal ecotype and two genotypes of an inland ecotype were planted at coastal and inland sites. After three months, we collected rhizosphere and bulk soil and assessed microbial communities by 16S rRNA gene sequencing. We found that local environment (coastal versus inland site) strongly influenced rhizosphere communities, at least in part due to distinct local microbial species pools. Host identity played a smaller role: at each site, the ecotypes exhibited remarkably similar composition of microbial communities at the class level, indicating that divergent M. guttatus ecotypes recruit phylogenetically similar rhizosphere communities, even in environments to which they are maladapted. Nevertheless, the two ecotypes significantly differed in community composition at the inland site due to an exclusive set of rare taxa associated with each ecotype. Although our results indicate that locally-adapted M. guttatus ecotypes are genetically diverged in factors shaping rhizosphere communities, environmental factors can trump genetic factors in shaping the M. guttatus microbiome. Overall, our findings demonstrate that wild plants strongly impact root-associated microbial communities, but hierarchical drivers interact to shape microbial community assembly outcomes.

scholarly journals Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4735 ◽  
Author(s):  
Angus Angermeyer ◽  
Sarah C. Crosby ◽  
Julie A. Huber
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Communities ◽  
Latitudinal Gradient ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Environmental Selection

Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex interplay between dispersal and environmental selection for microbial communities in nature.

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

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.

scholarly journals Structure of Microbial Communities When Complementary Effluents Are Anaerobically Digested

2021 ◽  
Vol 11 (3) ◽  
pp. 1293
Author(s):  
Ana Eusébio ◽  
André Neves ◽  
Isabel Paula Marques
Keyword(s):  
Anaerobic Digestion ◽  
Microbial Communities ◽  
Volatile Fatty Acids ◽  
Olive Mill Wastewater ◽  
Organic Load ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Olive Mill

Olive oil and pig productions are important industries in Portugal that generate large volumes of wastewater with high organic load and toxicity, raising environmental concerns. The principal objective of this study is to energetically valorize these organic effluents—piggery effluent and olive mill wastewater—through the anaerobic digestion to the biogas/methane production, by means of the effluent complementarity concept. Several mixtures of piggery effluent were tested, with an increasing percentage of olive mill wastewater. The best performance was obtained for samples of piggery effluent alone and in admixture with 30% of OMW, which provided the same volume of biogas (0.8 L, 70% CH4), 63/75% COD removal, and 434/489 L CH4/kg SVin, respectively. The validation of the process was assessed by molecular evaluation through Next Generation Sequencing (NGS) of the 16S rRNA gene. The structure of the microbial communities for both samples, throughout the anaerobic process, was characterized by the predominance of bacterial populations belonging to the phylum Firmicutes, mainly Clostridiales, with Bacteroidetes being the subdominant populations. Archaea populations belonging to the genus Methanosarcina became predominant throughout anaerobic digestion, confirming the formation of methane mainly from acetate, in line with the greatest removal of volatile fatty acids (VFAs) in these samples.

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