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

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.

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

10.1101/731828 ◽

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.

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Microbial community structure and performance of an anaerobic reactor digesting cassava pulp and pig manure

Water Science & Technology ◽

10.2166/wst.2012.358 ◽

2012 ◽

Vol 66 (7) ◽

pp. 1590-1600 ◽

Cited By ~ 14

Author(s):

P. Panichnumsin ◽

B. Ahring ◽

A. Nopharatana ◽

P. Chaiprasert

Keyword(s):

Community Structure ◽

Microbial Community ◽

Community Dynamics ◽

Denaturing Gradient Gel Electrophoresis ◽

Pig Manure ◽

Relative Distribution ◽

Cassava Pulp ◽

Microbial Community Dynamics ◽

Gradient Gel Electrophoresis ◽

Substrate Types

Microbial community dynamics in response to changes in substrate types (i.e. pig manure (PM), cassava pulp (CP) and mixtures of PM and CP) were investigated in an anaerobic continuously stirred tank reactor (CSTR). Molecular identification of bacterial and archaeal domains were performed, using a 16S rDNA clone library with polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) screening and phylogenetic analysis. Analysis of bacterial clone libraries revealed that the differences in the community structure corresponded to the substrate types. However, the Bacteroidetes were the most abundant group in all substrates, followed by the Clostridia. With pure PM, the dominant bacterial groups were Bacteroidales, Clostridia and Paludibacter. With a co-substrate, at CP to PM (CP:PM) ratio of 50:50, the sequences analysis revealed the greatest diversity of bacterial communities at class level, and the sequences affiliated with Cytophaga sp. became an exclusive predominant. With CP alone, Bacteroides sp. was the dominant species and this reactor had the lowest diversity of bacteria. Archaea observed in the CSTR fed with all substrate types were Methanosaeta sp., Methanosaeta concilii and Methanospirillum hungatei. Among the Archaea, Methanosaeta sp. was the exclusive predominant. The relative distribution of Archaea also changed regarding to the substrate types.

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Effect of Nutrient Periodicity on Microbial Community Dynamics

Applied and Environmental Microbiology ◽

10.1128/aem.72.5.3175-3183.2006 ◽

2006 ◽

Vol 72 (5) ◽

pp. 3175-3183 ◽

Cited By ~ 35

Author(s):

Militza Carrero-Colï¿½n ◽

Cindy H. Nakatsu ◽

Allan Konopka

Keyword(s):

Community Structure ◽

Microbial Community ◽

Growth Rates ◽

Community Dynamics ◽

Denaturing Gradient Gel Electrophoresis ◽

Pulse Interval ◽

Substrate Affinity ◽

Rrna Gene ◽

Similarity Coefficients ◽

Microbial Community Dynamics

ABSTRACT When microbes are subjected to temporal changes in nutrient availability, growth rate and substrate affinity can contribute to competitive fitness and thereby affect microbial community structure. This hypothesis was tested using planktonic bacterial communities exposed to nutrient additions at 1-, 3-, 7-, or 14-day intervals. Growth rates after nutrient addition were inversely proportional to the pulse interval and declined from 0.5 h−1 to 0.15 h−1 as the pulse interval increased from 1 to 14 days. The dynamics of community structure were monitored by 16S rRNA gene PCR-denaturing gradient gel electrophoresis. At pulse intervals of more than 1 day, the community composition continued to change over 130 days. Although replicate systems exposed to the same pulse interval were physiologically similar, their community compositions could exhibit as much dissimilarity (Dice similarity coefficients of <0.5) as did systems operated at different intervals. Bacteria were cultivated from the systems to determine if the physiological characteristics of individual members were consistent with the measured performance of the systems. The isolates fell into three bacterial divisions, Bacteroidetes, Proteobacteria, and Actinobacteria. In agreement with community results, bacteria isolated from systems pulsed every day with nutrients had higher growth rates and ectoaminopeptidase specific activities than isolates from systems pulsed every 14 days. However, the latter isolates did not survive starvation longer than those provided with nutrients every day. The present study demonstrates the dynamic nature of microbial communities exposed to even simple and regular environmental discontinuities when a substantial pool of species that can catabolize the limiting substrate is present.

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A Long-Standing Complex Tropical Dipole Shapes Marine Microbial Biogeography

Applied and Environmental Microbiology ◽

10.1128/aem.00614-18 ◽

2018 ◽

Vol 84 (18) ◽

Cited By ~ 3

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.

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Impact of process conditions on the microbial community dynamics and metabolite production kinetics of teff sourdough fermentations under bakery and laboratory conditions

Food Science & Nutrition ◽

10.1002/fsn3.690 ◽

2018 ◽

Vol 6 (6) ◽

pp. 1438-1455 ◽

Cited By ~ 6

Author(s):

Henning Harth ◽

Simon Van Kerrebroeck ◽

Luc De Vuyst

Keyword(s):

Microbial Community ◽

Community Dynamics ◽

Process Conditions ◽

Metabolite Production ◽

Laboratory Conditions ◽

Microbial Community Dynamics ◽

Production Kinetics ◽

Kinetics Of

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Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms

10.1101/2020.08.27.267492 ◽

2020 ◽

Author(s):

Alex Cheong ◽

Chad Johnson ◽

Hanxiao Wan ◽

Aiping Liu ◽

John Kernien ◽

...

Keyword(s):

Wound Healing ◽

Community Structure ◽

Microbial Community ◽

Community Dynamics ◽

Chronic Wound ◽

Recurrent Infection ◽

Priority Effects ◽

Chronic Infections ◽

Microbial Community Dynamics ◽

Host Microbe Interactions

AbstractA hallmark of chronic infections are polymicrobial biofilms. The forces governing assembly and maturation of these microbial ecosystems are largely unexplored but the consequences on host response and clinical outcome can be significant. In the context of wound healing, formation of a biofilm and a stable microbial community structure is associated with impaired tissue repair resulting in a non-healing chronic wound. These types of wounds can persist for years simmering below the threshold of classical clinical infection or cycling through phases of recurrent infection. In the most severe outcome amputation of lower extremities may occur if spreading infection ensues. Here we take an ecological perspective to study priority effects and competitive exclusion on overall biofilm community structure in a three-membered community of microbes derived from a chronic wound. We find that priority effects occur across both biotic and abiotic substrates, and ecological interactions can alter both fungal physiology and host inflammatory response. We show that bacterial-competition occurs for binding to fungal structures, and some species trigger the yeast-hyphae switch, resulting in enhanced neutrophil killing and inflammation. Collectively, the results presented here facilitate our understanding of fungal-bacterial microbial community dynamics and their effects on, host-microbe interactions, pathogenesis, and ultimately, wound healing.

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Correlation between microbial community structure and biofouling as determined by analysis of microbial community dynamics

Bioresource Technology ◽

10.1016/j.biortech.2015.08.049 ◽

2015 ◽

Vol 197 ◽

pp. 99-105 ◽

Cited By ~ 45

Author(s):

Xuechao Guo ◽

Yu Miao ◽

Bing Wu ◽

Lin Ye ◽

Haiyan Yu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Community Dynamics ◽

Microbial Community Dynamics

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Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature

Microorganisms ◽

10.3390/microorganisms9122425 ◽

2021 ◽

Vol 9 (12) ◽

pp. 2425

Author(s):

Hiie Nõlvak ◽

Nga Phuong Dang ◽

Marika Truu ◽

Angela Peeb ◽

Kertu Tiirik ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Crude Oil ◽

Microbial Community Structure ◽

Community Dynamics ◽

Oil Spills ◽

Hydrocarbon Degradation ◽

Taxonomic Assignment ◽

Metabolic Potential ◽

Microbial Community Dynamics

The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure, dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater. The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently, the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation. The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.

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