scholarly journals A Long-Standing Complex Tropical Dipole Shapes Marine Microbial Biogeography

2018 ◽  
Vol 84 (18) ◽  
Author(s):  
Wei Yan ◽  
Rui Zhang ◽  
Nianzhi Jiao
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Large Scale ◽  
Community Dynamics ◽  
Anticyclonic Eddy ◽  
Cyclonic Eddy ◽  
Content Type ◽  
Microbial Community Dynamics ◽  
Biogeographic Provinces

ABSTRACTMicrobial population size, production, diversity, and community structure are greatly influenced by the surrounding physicochemical conditions, such as large-scale biogeographic provinces and water masses. An oceanic mesoscale dipole consists of a cyclonic eddy and an anticyclonic eddy. Dipoles occur frequently in the ocean and usually last from a few days to several months; they have significant impacts on local and global oceanic biological, ecological, and geochemical processes. To better understand how dipoles shape microbial communities, we examined depth-resolved distributions of microbial communities across a dipole in the South China Sea. Our data demonstrated that the dipole had a substantial influence on microbial distributions, community structure, and functional groups both vertically and horizontally. Large alpha and beta diversity differences were observed between anticyclonic and cyclonic eddies in surface and subsurface layers, consistent with distribution changes of major bacterial groups in the dipole. The dipole created uplift, downward transport, enrichment, depletion, and horizontal transport effects. We also found that the edge of the dipole might induce strong subduction, indicated by the presence ofProchlorococcusandSynechococcusin deep waters. Our findings suggest that dipoles, with their unique characteristics, might act as a driver for microbial community dynamics.IMPORTANCEOceanic dipoles, which consist of a cyclonic eddy and an anticyclonic eddy together, are among the most contrasted phenomena in the ocean. Dipoles generate strong vertical mixing and horizontal advection, inducing biological responses. This study provides vertical profiles of microbial abundance, diversity, and community structure in a mesoscale dipole. We identify the links between the physical oceanography and microbial oceanography and demonstrate that the dipole, with its unique features, could act as a driver for microbial community dynamics, which may have large impacts on both the local and global marine biogeochemical cycles.

Linking Microbial Community Dynamics in BIOX® Leaching Tanks to Process Conditions: Integrating Lab and Commercial Experience

2017 ◽  
Vol 262 ◽  
pp. 38-42 ◽  
Author(s):  
Mariette Smart ◽  
Robert J. Huddy ◽  
Catherine J. Edward ◽  
Charl Fourie ◽  
Trust Shumba ◽  
...  
Keyword(s):  
South Africa ◽  
Community Structure ◽  
Microbial Community ◽  
Research University ◽  
Community Dynamics ◽  
Operating Conditions ◽  
Process Conditions ◽  
Significant Shift ◽  
Engineering Research ◽  
Microbial Community Dynamics

In the commercial BIOX® process, an acidophilic mixed bacterial and archaeal community dominated by iron and sulphur oxidising microorganisms is used to facilitate the recovery of precious metals from refractory gold-bearing sulphidic mineral concentrates. Characterisation of the microbial communities associated with commercial BIOX® reactors from four continents revealed a significant shift in the microbial community structure compared to that of the seed culture, maintained at SGS (South Africa). This has motivated more detailed study of the microbial community dynamics in the process. Microbial speciation of a subset of the BIOX® reactors at Fairview mines (Barberton, South Africa) and two laboratory maintained reactors housed at Centre for Bioprocess Engineering Research, University of Cape Town, has been performed tri-annually for three years by quantitative real-time polymerase chain reaction. The laboratory BIOX® culture maintained on Fairview concentrate was dominated by the desired iron oxidiser, Leptospirillum ferriphilum, and sulphur oxidiser, Acidithiobacillus caldus, when operated under standard BIOX® conditions. Shifts in the microbial community as a result of altered operating conditions were transient and did not result in a loss of the microbial diversity of the BIOX® culture. The community structure of the Fairview mines BIOX® reactor tanks showed archaeal dominance of these communities by organisms such as the iron oxidiser Ferroplasma acidiphilum and a Thermoplasma sp. for the period monitored. Shifts in the microbial community were observed across the monitoring period and mapped to changes in performance of the commercial process plant. Understanding the effect of changes in the plant operating conditions on the BIOX® community structure may assist in providing conditions that support the desired microbial consortium for optimal biooxidation to maximize gold recovery.

scholarly journals Visualizing Microbial Community Dynamics via a Controllable Soil Environment

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Arunima Bhattacharjee ◽  
Dusan Velickovic ◽  
Thomas W. Wietsma ◽  
Sheryl L. Bell ◽  
Janet K. Jansson ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Soil Core ◽  
Soil Microbial ◽  
Functional Relationships ◽  
Microbial Community Dynamics

ABSTRACT Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil. IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.

scholarly journals Analysis of Microbial Community Dynamics during the Acclimatization Period of a Membrane Bioreactor Treating Table Olive Processing Wastewater

2019 ◽  
Vol 9 (18) ◽  
pp. 3647 ◽  
Author(s):  
Sotiris I. Patsios ◽  
Sofia Michailidou ◽  
Konstantinos Pasentsis ◽  
Antonios M. Makris ◽  
Anagnostis Argiriou ◽  
...  
Keyword(s):  
Microbial Community ◽  
Biological Treatment ◽  
Large Scale ◽  
Membrane Bioreactor ◽  
Community Dynamics ◽  
Metabolic Adaptation ◽  
Process Step ◽  
Microbial Community Dynamics ◽  
Table Olive ◽  
Acclimatization Period

Biological treatment of table olive processing wastewater (TOPW) may be problematic due to its high organic and polyphenolic compound content. Biomass acclimatization is a necessary, yet sensitive, stage for efficient TOPW biological treatment. Next-generation sequencing technologies can provide valuable insights into this critical process step. An aerobic membrane bioreactor (MBR) system, initially inoculated with municipal activated sludge, was acclimatized to treat TOPW. Operational stability and bioremediation efficiency were monitored for approx. three months, whereas microbial community dynamics and metabolic adaptation were assessed through metagenomic and metatranscriptomic analysis. A swift change was identified in both the prokaryotic and eukaryotic bio-community after introduction of TOPW in the MBR, and a new diverse bio-community was established. Thauera and Paracoccus spp. are dominant contributors to the metabolic activity of the stable bio-community, which resulted in over 90% and 85% removal efficiency of total organic carbon and total polyphenols, respectively. This is the first study assessing the microbial community dynamics in a well-defined MBR process treating TOPW, offering guidance in the start-up of large-scale applications.

scholarly journals Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Ryan A. Blaustein ◽  
Graciela L. Lorca ◽  
Julie L. Meyer ◽  
Claudio F. Gonzalez ◽  
Max Teplitski
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Sequencing ◽  
Symptom Severity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
The Core ◽  
Symptom Progression

ABSTRACTStable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused byLiberibacter asiaticus,Liberibacter americanus, andLiberibacter africanus. The microbial communities of leaves (n= 94) and roots (n= 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance ofLiberibacterspp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship betweenLiberibacterspp. and members of theBurkholderiaceae,Micromonosporaceae, andXanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCEThis study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.

scholarly journals Microbial community dynamics in the forefield of glaciers

2014 ◽  
Vol 281 (1795) ◽  
pp. 20140882 ◽  
Author(s):  
James A. Bradley ◽  
Joy S. Singarayer ◽  
Alexandre M. Anesio
Keyword(s):  
Microbial Community ◽  
Large Scale ◽  
Community Dynamics ◽  
Microbial Community Composition ◽  
Future Research ◽  
Nutrient Pools ◽  
Microbial Community Dynamics ◽  
Ice Retreat ◽  
External Sources ◽  
Bacteria And Fungi

Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.

scholarly journals Geochemical and Temporal Influences on the Enrichment of Acidophilic Iron-Oxidizing Bacterial Communities

2016 ◽  
Vol 82 (12) ◽  
pp. 3611-3621 ◽  
Author(s):  
Yizhi Sheng ◽  
Kyle Bibby ◽  
Christen Grettenberger ◽  
Bradley Kaley ◽  
Jennifer L. Macalady ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Temporal Distance ◽  
Fed Batch ◽  
Content Type ◽  
Term Operation ◽  
Geochemical Conditions ◽  
Suspended Growth

ABSTRACTTwo acid mine drainage (AMD) sites in the Appalachian bituminous coal basin were selected to enrich for Fe(II)-oxidizing microbes and measure rates of low-pH Fe(II) oxidation in chemostatic bioreactors. Microbial communities were enriched for 74 to 128 days in fed-batch mode, then switched to flowthrough mode (additional 52 to 138 d) to measure rates of Fe(II) oxidation as a function of pH (2.1 to 4.2) and influent Fe(II) concentration (80 to 2,400 mg/liter). Biofilm samples were collected throughout these operations, and the microbial community structure was analyzed to evaluate impacts of geochemistry and incubation time. Alpha diversity decreased as the pH decreased and as the Fe(II) concentration increased, coincident with conditions that attained the highest rates of Fe(II) oxidation. The distribution of the seven most abundant bacterial genera could be explained by a combination of pH and Fe(II) concentration.Acidithiobacillus,Ferrovum,Gallionella,Leptospirillum,Ferrimicrobium,Acidiphilium, andAcidocellawere all found to be restricted within specific bounds of pH and Fe(II) concentration. Temporal distance, defined as the cumulative number of pore volumes from the start of flowthrough mode, appeared to be as important as geochemical conditions in controlling microbial community structure. Both alpha and beta diversities of microbial communities were significantly correlated to temporal distance in the flowthrough experiments. Even after long-term operation under nearly identical geochemical conditions, microbial communities enriched from the different sites remained distinct. While these microbial communities were enriched from sites that displayed markedly different field rates of Fe(II) oxidation, rates of Fe(II) oxidation measured in laboratory bioreactors were essentially the same. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup.IMPORTANCEThis study showed that different microbial communities enriched from two sites maintained distinct microbial community traits inherited from their respective seed materials. Long-term operation (up to 128 days of fed-batch enrichment followed by up to 138 days of flowthrough experiments) of these two systems did not lead to the same, or even more similar, microbial communities. However, these bioreactors did oxidize Fe(II) and remove total iron [Fe(T)] at very similar rates. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup. This would be advantageous, because system performance should be well constrained and predictable for many different sites.

scholarly journals Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry

mSphere ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Zishu Liu ◽  
Nicolas Cichocki ◽  
Fabian Bonk ◽  
Susanne Günther ◽  
Florian Schattenberg ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Microbial Community ◽  
Microbial Communities ◽  
Temporal Resolution ◽  
Community Dynamics ◽  
Well Being ◽  
High Temporal Resolution ◽  
Ecological Stability ◽  
Stability Properties ◽  
Microbial Community Dynamics

Microbial communities drive many processes which affect human well-being directly, as in the human microbiome, or indirectly, as in natural environments or in biotechnological applications. Due to their complexity, their dynamics over time is difficult to monitor, and current sequence-based approaches are limited with respect to the temporal resolution. However, in order to eventually control microbial community dynamics, monitoring schemes of high temporal resolution are required. Flow cytometry provides single-cell-based data in the required temporal resolution, and we here use such data to compute stability properties as easy to interpret univariate indicators of microbial community dynamics. Such monitoring tools will allow for a fast, continuous, and cost-effective screening of stability states of microbiomes. Applicable to various environments, including bioreactors, surface water, and the human body, it will contribute to the development of control schemes to manipulate microbial community structures and performances.

scholarly journals Constrained proteome allocation affects coexistence in models of competitive microbial communities

2020 ◽  
Author(s):  
Leonardo Pacciani-Mori ◽  
Samir Suweis ◽  
Amos Maritan ◽  
Andrea Giometto
Keyword(s):  
Population Dynamics ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Bacterial Strains ◽  
Theoretical Frameworks ◽  
Microbial Community Dynamics ◽  
Common Resource ◽  
Multiple Species ◽  
Consumer Resource

Microbial communities are ubiquitous and play crucial roles in many natural processes. Despite their importance for the environment, industry and human health, there are still many aspects of microbial community dynamics that we do not understand quantitatively. Recent experiments have shown that the metabolism of species in a community is intertwined with its composition, suggesting that properties at the intracellular level such as the allocation of cellular proteomic resources must be taken into account when describing microbial communities with a population dynamics approach. In this work we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur’s consumer-resource model, in light of experimental evidence showing how pro-teome allocation affects microbial growth. This new framework allows us to describe community dynamics at an intermediate level of complexity between classical consumer-resource models and biochemical models of microbial metabolism, accounting for temporally-varying proteome allocation subject to constraints on growth and protein synthesis in the presence of multiple resources, while preserving analytical insight into the dynamics of the system. We first show experimentally that proteome allocation needs to be accounted for to properly understand the dynamics of even the simplest microbial community, i.e. two bacterial strains competing for one common resource. We then study the model analytically and numerically to determine the conditions that allow multiple species to coexist in systems with arbitrary numbers of species and resources.

scholarly journals Reproducible microbial community dynamics of two drinking water systems treating similar source waters

2019 ◽  
Author(s):  
Sarah C Potgieter ◽  
Ameet J Pinto ◽  
Minette Havenga ◽  
Makhosazana Sigudu ◽  
Stefanus N Venter
Keyword(s):  
Drinking Water ◽  
Microbial Community ◽  
Microbial Communities ◽  
Surface Waters ◽  
Distribution Systems ◽  
Community Dynamics ◽  
Microbial Community Dynamics ◽  
Two Systems ◽  
The Impact ◽  
Source Waters

AbstractIn addition to containing higher concentrations of organics and bacterial cells, surface waters are often more vulnerable to pollution and microbial contamination with intensive industrial and agricultural activities frequently occurring in areas surrounding the water source. Therefore, surface waters typically require additional treatment, where the choice of treatment strategy is critical for water quality. Using 16S rRNA gene profiling, this study provides a unique opportunity to simultaneously investigate and compare two drinking water treatment plants and their corresponding distribution systems. The two treatment plants treat similar surface waters, from the same river system, with the same sequential treatment strategies. Here, the impact of treatment and distribution on the microbial community within and between each system was compared over an eight-month sampling campaign. Overall, reproducible spatial and temporal dynamics within both DWTPs and their corresponding DWDSs were observed. Although source waters showed some dissimilarity in microbial community structure and composition, pre-disinfection treatments (i.e. coagulation, flocculation, sedimentation and filtration) resulted in highly similar microbial communities between the filter effluent samples. This indicated that the same treatments resulted in the development of similar microbial communities. Conversely, post-disinfection (i.e. chlorination and chloramination) resulted in increased dissimilarity between disinfected samples from the two systems, showing alternative responses of the microbial community to disinfection. Lastly, it was observed that within the distribution system the same dominant taxa were selected where samples increased in similarity with increased residence time. Although, differences were found between the two systems, overall treatment and distribution had a similar impact on the microbial community in each system. This study therefore provides valuable information on the impact of treatment and distribution on the drinking water microbiome.HighlightsSource waters show some dissimilarity in microbial community.Treatment processes increases similarity and selects for the same dominant taxa.Differential response to chlorination causing increased dissimilarity and variation.Stabilisation of DWDS microbial community through selection of same dominant taxa.Microbial community dynamics are reproducible between the two systems.

scholarly journals Microbial diversity of the Arabian Sea in the Oxygen minimum zones by metagenomics approach

2019 ◽  
Author(s):  
Mandar S. Paingankar ◽  
Kedar Ahire ◽  
Pawan Mishra ◽  
Shriram Rajpathak ◽  
Deepti D. Deobagkar
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Arabian Sea ◽  
Community Dynamics ◽  
Oxygen Depletion ◽  
Oxygen Minimum Zones ◽  
Microbial Community Dynamics ◽  
Nitrate Reducers ◽  
Insight Into ◽  
Oxygen Minimum

ABSTRACTLarge oxygen depleted areas known as oxygen minimum zones (OMZ) have been observed in the Arabian Sea and recent reports indicate that these areas are expanding at an alarming rate. In marine waters, oxygen depletion may also be related to global warming and the temperature rise, acidification and deoxygenation can lead to major consequences wherein the plants, fish and other biota will struggle to survive in the ecosystem.The current study has identified the microbial community structure using NGS based metagenomics analysis in the water samples collected at different depth from the oxygen depleted and non-OMZ areas of Arabian Sea. Environmental variables such as depth, site of collection and oxygen concentration appeared to influence the species richness and evenness among microbial communities in these locations. Our observations clearly indicate that population dynamics of microbes consisting of nitrate reducers accompanied by sulphate reducers and sulphur oxidizers participate in the interconnected geochemical cycles of the OMZ areas. In addition to providing baseline data related to the diversity and microbial community dynamics in oxygen-depleted water in the OMZ; such analysis can provide insight into processes regulating productivity and ecological community structure of the ocean.

Sign in / Sign up

Export Citation Format

Share Document