The formation and fate of organoarsenic species in marine ecosystems: do existing experimental approaches appropriately simulate ecosystem complexity?

2015 ◽  
Vol 12 (2) ◽  
pp. 149 ◽  
Author(s):  
Elliott G. Duncan ◽  
William A. Maher ◽  
Simon D. Foster

Environmental context In marine environments, inorganic arsenic present in seawater is transformed to organoarsenic species, mainly arsenoribosides in algae and arsenobetaine in animals. These transformations decrease the toxicity of arsenic, yet the fate of arsenoribosides and arsenobetaine when marine organisms decompose is unknown. We review the current literature on the degradation of these organoarsenic species in marine systems detailing the drivers behind their degradation, and also discuss the environmental relevance of laboratory-based experiments. Abstract Despite arsenoribosides and arsenobetaine (AB) being the major arsenic species in marine macro-algae and animals they have never been detected in seawater. In all studies reviewed arsenoribosides from marine macro-algae were degraded to thio-arsenoribosides, dimethylarsinoylethanol (DMAE), dimethylarsenate (DMA), methylarsenate (MA) with arsenate (AsV) the final product of degradation. The use of different macro-algae species and different experimental microcosms did not influence the arsenoriboside degradation pathway. The use of different experimental approaches, however, did influence the rate and extent at which arsenoriboside degradation occurred. This was almost certainly a function of the complexity of the microbial community within the microcosm, with greater complexity resulting in rapid and more complete arsenoriboside degradation. AB from decomposing animal tissues is degraded to trimethylarsine oxide (TMAO) or dimethylarsenoacetate (DMAA), DMA and finally AsV. The degradation of AB unlike arsenoribosides occurs via a dual pathway with environmental or microbial community variability influencing the pathway taken. The environmental validity of different experimental approaches used to examine the fate of organoarsenic species was also reviewed. It was evident that although liquid culture incubation studies are cheap and reproducible they lack the ability to culture representative microbial communities. Microcosm studies that include sand and sediment are more environmentally representative as they are a better simulation of marine ecosystems and are also likely to facilitate complex microbial communities. An added benefit of microcosm studies is that they are able to be run in parallel with field-based research to provide a holistic assessment of the degradation of organoarsenic species in marine environments.


2014 ◽  
Vol 11 (3) ◽  
pp. 289 ◽  
Author(s):  
Elliott G. Duncan ◽  
William A. Maher ◽  
Simon D. Foster ◽  
Frank Krikowa ◽  
Katarina M. Mikac

Environmental context Arsenoribosides are the major arsenic species in marine macro-algae, yet inorganic arsenic is the major arsenic species found in seawater. We investigated the degradation of arsenoribosides associated with Ecklonia radiata by the use of microcosms containing both natural and autoclaved seawater and sand. The decomposition and persistence of arsenic species was linked to the use of autoclaved seawater and sand, which suggests that arsenoriboside degradation is governed by the microbial composition of microenvironments within marine systems. Abstract We investigated the influence of microbial communities on the degradation of arsenoribosides from E. radiata tissues decomposing in sand and seawater-based microcosms. During the first 30 days, arsenic was released from decomposing E. radiata tissues into seawater and sand porewaters in all microcosms. In microcosms containing autoclaved seawater and autoclaved sand, arsenic was shown to persist in soluble forms at concentrations (9–18µg per microcosm) far higher than those present initially (~3µg per microcosm). Arsenoribosides were lost from decomposing E. radiata tissues in all microcosms with previously established arsenoriboside degradation products, such as thio-arsenic species, dimethylarsinoylethanol (DMAE), dimethylarsenate (DMA) and arsenate (AsV) observed in all microcosms. DMAE and DMA persisted in the seawater and sand porewaters of microcosms containing autoclaved seawater and autoclaved sand. This suggests that the degradation step from arsenoribosides → DMAE occurs on algal surfaces, whereas the step from DMAE → AsV occurs predominantly in the water-column or sand–sediments. This study also demonstrates that disruptions to microbial connectivity (defined as the ability of microbes to recolonise vacant habitats) result in alterations to arsenic cycling. Thus, the re-cycling of arsenoribosides released from marine macro-algae is driven by microbial complexity plus microbial connectivity rather than species diversity as such, as previously assumed.



mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sara Gushgari-Doyle ◽  
Ronald S. Oremland ◽  
Ray Keren ◽  
Shaun M. Baesman ◽  
Denise M. Akob ◽  
...  

ABSTRACT In aquifers, acetylene (C2H2) is a product of abiotic degradation of trichloroethene (TCE) catalyzed by in situ minerals. C2H2 can, in turn, inhibit multiple microbial processes including TCE dechlorination and metabolisms that commonly support dechlorination, in addition to supporting the growth of acetylenotrophic microorganisms. Previously, C2H2 was shown to support TCE reductive dechlorination in synthetic, laboratory-constructed cocultures containing the acetylenotroph Pelobacter sp. strain SFB93 and Dehalococcoides mccartyi strain 195 or strain BAV1. In this study, we demonstrate TCE and perchloroethene (PCE) reductive dechlorination by a microbial community enriched from contaminated groundwater and amended with C2H2 as the sole electron donor and organic carbon source. The metagenome of the stable, enriched community was analyzed to elucidate putative community functions. A novel anaerobic acetylenotroph in the phylum Actinobacteria was identified using metagenomic analysis. These results demonstrate that the coupling of acetylenotrophy and reductive dechlorination can occur in the environment with native bacteria and broaden our understanding of biotransformation at contaminated sites containing both TCE and C2H2. IMPORTANCE Understanding the complex metabolisms of microbial communities in contaminated groundwaters is a challenge. PCE and TCE are among the most common groundwater contaminants in the United States that, when exposed to certain minerals, exhibit a unique abiotic degradation pathway in which C2H2 is a product. C2H2 can act as both an inhibitor of TCE dechlorination and of supporting metabolisms and an energy source for acetylenotrophic bacteria. Here, we combine laboratory microcosm studies with computational approaches to enrich and characterize an environmental microbial community that couples two uncommon metabolisms, demonstrating unique metabolic interactions only yet reported in synthetic, laboratory-constructed settings. Using this comprehensive approach, we have identified the first reported anaerobic acetylenotroph in the phylum Actinobacteria, demonstrating the yet-undescribed diversity of this metabolism that is widely considered to be uncommon.



2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.





2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  

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.



2021 ◽  
Vol 13 (13) ◽  
pp. 7358
Author(s):  
Dong-Hyun Kim ◽  
Hyun-Sik Yun ◽  
Young-Saeng Kim ◽  
Jong-Guk Kim

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.



Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 173
Author(s):  
Huiling Guan ◽  
Jiangwen Fan ◽  
Haiyan Zhang ◽  
Warwick Harris

Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.



2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zala Schmautz ◽  
Carlos A. Espinal ◽  
Andrea M. Bohny ◽  
Fabio Rezzonico ◽  
Ranka Junge ◽  
...  

Abstract Background An aquaponic system couples cultivation of plants and fish in the same aqueous medium. The system consists of interconnected compartments for fish rearing and plant production, as well as for water filtration, with all compartments hosting diverse microbial communities, which interact within the system. Due to the design, function and operation mode of the individual compartments, each of them exhibits unique biotic and abiotic conditions. Elucidating how these conditions shape microbial communities is useful in understanding how these compartments may affect the quality of the water, in which plants and fish are cultured. Results We investigated the possible relationships between microbial communities from biofilms and water quality parameters in different compartments of the aquaponic system. Biofilm samples were analyzed by total community profiling for bacterial and archaeal communities. The results implied that the oxygen levels could largely explain the main differences in abiotic parameters and microbial communities in each compartment of the system. Aerobic system compartments are highly biodiverse and work mostly as a nitrifying biofilter, whereas biofilms in the anaerobic compartments contain a less diverse community. Finally, the part of the system connecting the aerobic and anaerobic processes showed common conditions where both aerobic and anaerobic processes were observed. Conclusion Different predicted microbial activities for each compartment were found to be supported by the abiotic parameters, of which the oxygen saturation, total organic carbon and total nitrogen differentiated clearly between samples from the main aerobic loop and the anaerobic compartments. The latter was also confirmed using microbial community profile analysis.



Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 865
Author(s):  
Lantian Su ◽  
Xinxin Liu ◽  
Guangyao Jin ◽  
Yue Ma ◽  
Haoxin Tan ◽  
...  

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.



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