1
|
Wang X, Wang T, Meng H, Xing F, Yun H. Anammox process in anaerobic baffled biofilm reactors with columnar packings: Characteristics of flow field and microbial community. CHEMOSPHERE 2024; 355:141774. [PMID: 38522670 DOI: 10.1016/j.chemosphere.2024.141774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/29/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
The enrichment of anammox bacteria is a key issue in the application of anammox processes. A new type of reactor - anaerobic baffle biofilm reactor (ABBR) developed from anaerobic baffle reactor (ABR) was filled with columnar packings and established for effective enrichment of anammox bacteria. The flow field analysis showed that, compared with ABR, ABBR narrowed the dead zone so as to improve the substrate transferring performances. Two ABBRs with different types of columnar packings (Packings 1 and Packings 2) were constructed to culture anammox biofilms. Packings 1 consisted of the single-form honeycomb carriers while Packings 2 was modular composite packings consisting of non-woven fabric and honeycomb carriers. The effects of different types of columnar packings on microbial community and nitrogen removal were studied. The ABBR filled with Packings 2 had a higher retention rate of biomass than the ABBR filled with Packings 1, making the anammox start-up period be shortened by 21.28%. The enrichment of anammox bacteria were achieved and the dominant anammox bacteria were Candidatus Brocadia in both R1 and R2. However, there were four genera of anammox bacteria in R2 and one genus of anammox bacteria in R1, and the cell density of anammox bacteria in R2 was 95% higher than that in R1. R2 has the advantage of maintaining excellent and stable nitrogen removal performance at high nitrogen loading rate. The results revealed that the packings composed of two types of carriers may have a better enrichment effect on anammox bacteria. This study is of great significance for the rapid enrichment of anammox bacteria and the technical promotion of anammox process.
Collapse
Affiliation(s)
- Xian Wang
- Department of Environmental Engineering, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| | - Tao Wang
- Department of Environmental Engineering, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China.
| | - Hao Meng
- Department of Environmental Engineering, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| | - Fanghua Xing
- Department of Environmental Engineering, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| | - Hongying Yun
- Department of Environmental Engineering, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| |
Collapse
|
2
|
Liu Y, Jin X, Huang S, Liu Y, Kong Z, Wu L, Ge G. Co-Occurrence Patterns of Soil Fungal and Bacterial Communities in Subtropical Forest-Transforming Areas. Curr Microbiol 2024; 81:64. [PMID: 38225342 DOI: 10.1007/s00284-023-03608-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 09/30/2021] [Indexed: 01/17/2024]
Abstract
Soil microbial communities are engineers of important biogeochemical processes and play a critical role in regulating the functions and stability of forest ecosystem. However, few studies have assessed microbial interactions during forest conversion, which is essential to the understanding of the structure and function of soil microbiome. Herein, we investigated the co-occurrence network pattern and putative functions of fungal and bacterial communities in forest-transforming areas (five sites that cover the typical forests) using high-throughput sequencing of the ITS genes and 16S rRNA. Our study showed that the bacterial network had higher average connectivity and more links than fungal network, which might indicate that the bacterial community had more complex internal interactions compared with fungal one. Alphaproteobacteria_unclassfied, Telmatobacter, 0319-6A21 and Latescibacteria_unclassfied were the keystone taxa in bacterial network. For the fungal community network, the keystone taxon was Ceratobasidium. A structural equation model indicated that the available potassium and total organic carbon were important soil environmental factors, which affected all microbial modules, including bacterial and fungi. Total nitrogen had significant effects on the bacterial module that contains a relatively rich group of nitrogen cycling functions, and pH influenced the bacterial module which have higher potential functions of carbon cycling. And, more fungal modules were directly affected by forest structure (S Tree) compared with bacterial ones. This study provides new insights into our understanding of the feedback of underground creatures to forest conversion and highlights the importance of microbial modules in the nutrient cycling process.
Collapse
Affiliation(s)
- Yajun Liu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Xin Jin
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Shihao Huang
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Yizhen Liu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Zhaoyu Kong
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China.
| | - Gang Ge
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang, 330031, China
| |
Collapse
|
3
|
Aguilera-Huertas J, Cuartero J, Ros M, Pascual JA, Parras-Alcántara L, González-Rosado M, Özbolat O, Zornoza R, Egea-Cortines M, Hurtado-Navarro M, Lozano-García B. How binomial (traditional rainfed olive grove-Crocus sativus) crops impact the soil bacterial community and enhance microbial capacities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118572. [PMID: 37421720 DOI: 10.1016/j.jenvman.2023.118572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/26/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023]
Abstract
Intercropping can favour the yield of the main crop. However, because of the potential competition among woody crops, this system is rarely used by farmers. To increase knowledge about the intercropping system, we have explored three different combinations of alley cropping in rainfed olive groves compared to conventional management (CP): (i) Crocus sativus (D-S); (ii) Vicia sativa/Avena sativa in annual rotation (D-O); and (iii) Lavandula x intermedia (D-L). Different soil chemical properties were analyzed to evaluate the effects of alley cropping, while 16S rRNA amplification and enzymatic activities were determined to study the changes that occurred in soil microbial communities and activity. In addition, the influence of intercropping on the potential functionality of the soil microbial community was measured. Data revealed that the intercropping systems highly affected the microbial community and soil properties. The D-S cropping system increased soil total organic carbon and total nitrogen that were correlated with the bacterial community, indicating that both parameters were the main drivers shaping the structure of the bacterial community. The D-S soil cropping system had significantly higher relative abundances of the phyla Bacteroidetes, Proteobacteria, and Patescibacteria compared to the other systems and the genera Adhaeribacter, Arthrobacter, Rubellimicrobium, and Ramlibacter, related to C and N functions. D-S soil was also related to the highest relative abundances of Pseudoarthrobacter and Haliangium, associated with the plant growth-promoting effect, antifungal activity, and a potential P solubilizer. A potentially increase of C fixation and N fixation in soils was also observed in the D-S cropping system. These positive changes were related to the cessation of tillage and the development of a spontaneous cover crop, which increased soil protection. Thus, management practices that contribute to increasing soil cover should be encouraged to improve soil functionality.
Collapse
Affiliation(s)
- Jesús Aguilera-Huertas
- SUMAS Research Group, Department of Agricultural Chemistry, Soil Science and Microbiology, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, 14071, Cordoba, Spain
| | - Jessica Cuartero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903, Birmensdorf, Switzerland; Grupo de Enzimología y Biorremediación de suelos y residuos Orgánicos. Centro de Edafología y Biología aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Margarita Ros
- Grupo de Enzimología y Biorremediación de suelos y residuos Orgánicos. Centro de Edafología y Biología aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Jose Antonio Pascual
- Grupo de Enzimología y Biorremediación de suelos y residuos Orgánicos. Centro de Edafología y Biología aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Luis Parras-Alcántara
- SUMAS Research Group, Department of Agricultural Chemistry, Soil Science and Microbiology, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, 14071, Cordoba, Spain
| | - Manuel González-Rosado
- SUMAS Research Group, Department of Agricultural Chemistry, Soil Science and Microbiology, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, 14071, Cordoba, Spain; Department of Agricultural Science, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, 30203, Cartagena, Spain
| | - Onurcan Özbolat
- Department of Agricultural Science, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, 30203, Cartagena, Spain; Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Plaza del Hospital s/n, 30202, Cartagena, Spain
| | - Raúl Zornoza
- Department of Agricultural Science, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, 30203, Cartagena, Spain; Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Plaza del Hospital s/n, 30202, Cartagena, Spain
| | - Marcos Egea-Cortines
- Department of Agricultural Science, Universidad Politécnica de Cartagena, Paseo Alfonso XIII 48, 30203, Cartagena, Spain; Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Plaza del Hospital s/n, 30202, Cartagena, Spain
| | - María Hurtado-Navarro
- Grupo de Enzimología y Biorremediación de suelos y residuos Orgánicos. Centro de Edafología y Biología aplicada del Segura (CEBAS-CSIC), Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Beatriz Lozano-García
- SUMAS Research Group, Department of Agricultural Chemistry, Soil Science and Microbiology, Faculty of Science, Agrifood Campus of International Excellence - ceiA3, University of Cordoba, 14071, Cordoba, Spain.
| |
Collapse
|
4
|
Costa GMD, Costa SS, Baraúna RA, Castilho BP, Pinheiro IC, Silva A, Schaan AP, Ribeiro-Dos-Santos Â, Graças DAD. Effects of Degradation on Microbial Communities of an Amazonian Mangrove. Microorganisms 2023; 11:1389. [PMID: 37374891 DOI: 10.3390/microorganisms11061389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023] Open
Abstract
Mangroves provide a unique ecological environment for complex microbial communities, which play important roles in biogeochemical cycles, such as those for carbon, sulfur, and nitrogen. Microbial diversity analyses of these ecosystems help us understand the changes caused by external influences. Amazonian mangroves occupy an area of 9000 km2, corresponding to 70% of the mangroves in Brazil, on which studies of microbial biodiversity are extremely scarce. The present study aimed to determine changes in microbial community structure along the PA-458 highway, which fragmented a mangrove zone. Mangrove samples were collected from three zones, (i) degraded, (ii) in the process of recovery, and (iii) preserved. Total DNA was extracted and submitted for 16S rDNA amplification and sequencing on an MiSeq platform. Subsequently, reads were processed for quality control and biodiversity analyses. The most abundant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all three mangrove locations, but in significantly different proportions. We observed a considerable reduction in diversity in the degraded zone. Important genera involved in sulfur, carbon, and nitrogen metabolism were absent or dramatically reduced in this zone. Our results show that human impact in the mangrove areas, caused by the construction of the PA-458 highway, has resulted in a loss of biodiversity.
Collapse
Affiliation(s)
- Gleyciane Machado da Costa
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Sávio Souza Costa
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Rafael Azevedo Baraúna
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Bruno Pureza Castilho
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
| | - Izabel Cruz Pinheiro
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
| | - Artur Silva
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Ana Paula Schaan
- Laboratory of Medical and Human Genetics, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Medical and Human Genetics, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Diego Assis das Graças
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| |
Collapse
|
5
|
Hillyer KE, Raes E, Bissett A, Beale DJ. Multi-omics eco-surveillance of bacterial community function in legacy contaminated estuary sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120857. [PMID: 36513173 DOI: 10.1016/j.envpol.2022.120857] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Complex legacy contamination is a major issue for many estuaries, with toxicity affecting change in bacterial communities, and their provision of associated goods and services. Sequencing surveys of bacterial community composition provide inferred function; however, additional insights may be generated by measurement of realised metabolic phenotypes. We apply multi-omics (genomics, lipidomics, and metabolomics), with traditional sediment quality analyses, to characterise sediment-associated bacterial communities in an estuary subject to legacy metal contamination (Zn, Hg, As, Cd, Cu and Pb). Analyses of bacterial composition and inferred function (genomics) are coupled with measurements of realised bacterial phenotype (metabolomics and lipidomics) at multiple industrialised and reference sites. At sites with the highest sediment metal concentrations (NTB), we also observed increased abundances of hydrocarbon and sulphuric acid metabolites, indicating additional sediment contamination. Bacterial phyla across sampled sites were dominated by Proteobacteria and Desulfobacteria. NTB sites were enriched with metabolically versatile, cooperative and biofilm forming phyla including, Zixibacteria, Spirochaetota, SAR324 clade, Proteobacteria, Latescibacterota, Desulfobacterota, Deferrisomtota and Acidobateriota; with inferred functions characterised by sulphur metabolism, pathways associated with the degradation of complex organic molecules, and fermentation. Reference sites were characterised by enhanced vitamin biosynthesis, cell wall, cofactor and carbohydrate biosynthesis, and CO2 fixation. Measured metabolic phenotypes at NTB sites supported predicted functions, with most consistent change observed to naphthalene and aminobenzoate degradation pathways and carbohydrate metabolism (galactose, amino and nucleotide sugar). Change in NTB metabolite profiles was most highly correlated with sediment Hg concentrations, indicative of toxic exposure and potential for Hg methylation. Lipid profiles generated further insight into potential functional (hydroxy fatty acids) and community level change (ceramide phosphoethanolamines, unsaturated glycerides). Multi-omics outputs provided insights into bacterial community functions, modes of contaminant toxicity and expressed mechanisms of adaptation, necessary to better inform management decisions and predictive models in increasingly human-influenced environments.
Collapse
Affiliation(s)
- Katie E Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Eric Raes
- Oceans and Atmosphere, CSIRO, Battery Point, Hobart, TAS, Australia; Flourishing Oceans, Minderoo Foundation, Broadway, Nedlands, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO, Battery Point, Hobart, TAS, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, Australia.
| |
Collapse
|
6
|
Srivastava A, Verma D. Ganga River sediments of India predominate with aerobic and chemo-heterotrophic bacteria majorly engaged in the degradation of xenobiotic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:752-772. [PMID: 35904740 DOI: 10.1007/s11356-022-22198-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Sediment provides a stagnant habitat to microbes that accumulate organic matter and other industrial pollutants from the upper layer of the water. The sediment of the Ganga River of India is overlooked for exploring the bacterial diversity despite their taxon richness over the water counterpart. To enrich the limited information on the bacterial diversity of the Ganga River sediment, the present study was planned that relies on amplicon-based bacterial diversity of the Ganga River sediment by using bacterial-specific 16S hypervariable region (V3-V4). The Illumina MiSeq2500 platform generated 1,769,226 raw reads from the metagenomes of various samples obtained from ten sites in five major cities of Uttar Pradesh and Uttarakhand regions traversing the Ganga River. Taxonomy level analysis assigned 58 phyla, 366 order, and 715 genera of bacterial type. The high values of various diversity indices (Chao1, Shannon, and Simpson) in Kanpur sediment indicate the high bacterial richness compared to the Rishikesh sediment. However, several other ecological parameters (Shannon index, Simpson index, enspie _vector, and Faith_pd) were comparatively higher in Rishikesh sediment which is a comparatively less disturbed region by human activities over the other sediments samples studied here. Ganga River sediment dominates with Gram-negative, chemo-heterotrophic, and aerobic bacteria that chiefly belong to Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidota. The abundance of Nitrospira, Hydrogenophaga, Thauera, Vicinamibacteraceae, and Latescibacterota in the Ganga River sediment could be considered as the ecological indicators that find a significant role in the degradation of xenobiotic compounds. The PICRUSt-based analysis showed that ~ 35% of genes were involved in benzoate and aminobenzoate degradation where a significant portion of genes belong to nitrotoluene degradation (14%). Thus, the study uncovers a new perspective in the lineage of bacterial communities and their functional characterization of the Ganga River sediment.
Collapse
Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India, 226025
| | - Digvijay Verma
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India, 226025.
| |
Collapse
|
7
|
Chaudhary DK, Karki HP, Bajagain R, Kim H, Rhee TS, Hong JK, Han S, Choi YG, Hong Y. Mercury and other trace elements distribution and profiling of microbial community in the surface sediments of East Siberian Sea. MARINE POLLUTION BULLETIN 2022; 185:114319. [PMID: 36343547 DOI: 10.1016/j.marpolbul.2022.114319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
In this study, total mercury (THg), methylmercury (MeHg), various trace elements, and microbial communities were measured in surface sediments of the East Siberian Sea (ESS). The results showed that the average values of THg and MeHg were 58.8 ± 15.21 μg/kg and 0.50 ± 0.22 μg/kg, respectively. The notable levels of trace elements present in both surface sediment and porewater were Al, Fe, and Mn. The enrichment factor and geoaccumulation index analyses found that both natural phenomena and anthropogenic activities contributed to elevated concentrations of metals in the ESS. The redox proxy metals, pH, and SO42- were the major factors influencing the THg and MeHg distributions. Microbial profiles were substantially affected by metals and other abiotic factors. Proteobacteria and Thaumarchaeota were the most abundant phyla. Overall, the findings presented here facilitate the understanding of the current status of metal contamination, its influencing factors, and metal-microbiota-interactions in ESS.
Collapse
Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Hem Prakash Karki
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Rishikesh Bajagain
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Hwansuk Kim
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Tae Siek Rhee
- Korea Polar Research Institute, 26 Songdomirae-ro, Incheon 21990, Republic of Korea
| | - Jong Kuk Hong
- Korea Polar Research Institute, 26 Songdomirae-ro, Incheon 21990, Republic of Korea
| | - Seunghee Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Young-Gyun Choi
- Department of Environmental Engineering, Chungnam National University, Daejeon City, Republic of Korea
| | - Yongseok Hong
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea.
| |
Collapse
|
8
|
Shang Z, Wang Y, An M, Chen X, Kulyar MFEA, Tan Z, Liu S, Li K. The successional trajectory of bacterial and fungal communities in soil are fabricated by yaks’ excrement contamination in plateau, China. Front Microbiol 2022; 13:1016852. [DOI: 10.3389/fmicb.2022.1016852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
The soil microbiome is crucial in determining contemporary realistic conditions for future terrestrial ecological and evolutionary development. However, the precise mechanism between the fecal deposition in livestock grazing and changes in the soil microbiome remains unknown. This is the first in-depth study of bacterial and fungal taxonomic changes of excrement contaminated soils in the plateau (>3,500 m). This suggests the functional shifts towards a harmful-dominated soil microbiome. According to our findings, excrement contamination significantly reduced the soil bacterial and fungal diversity and richness. Furthermore, a continuous decrease in the relative abundance of microorganisms was associated with nutrient cycling, soil pollution purification, and root-soil stability with the increasing degree of excrement contamination. In comparison, soil pathogens were found to have the opposite trend in the scenario, further deteriorating normal soil function and system resilience. Such colonization and succession of the microbiome might provide an important potential theoretical instruction for microbiome-based soil health protection measures in the plateau of China.
Collapse
|
9
|
Deng L, Meile C, Fiskal A, Bölsterli D, Han X, Gajendra N, Dubois N, Bernasconi SM, Lever MA. Deposit-feeding worms control subsurface ecosystem functioning in intertidal sediment with strong physical forcing. PNAS NEXUS 2022; 1:pgac146. [PMID: 36714871 PMCID: PMC9802194 DOI: 10.1093/pnasnexus/pgac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/25/2022] [Indexed: 06/18/2023]
Abstract
Intertidal sands are global hotspots of terrestrial and marine carbon cycling with strong hydrodynamic forcing by waves and tides and high macrofaunal activity. Yet, the relative importance of hydrodynamics and macrofauna in controlling these ecosystems remains unclear. Here, we compare geochemical gradients and bacterial, archaeal, and eukaryotic gene sequences in intertidal sands dominated by subsurface deposit-feeding worms (Abarenicola pacifica) to adjacent worm-free areas. We show that hydrodynamic forcing controls organismal assemblages in surface sediments, while in deeper layers selective feeding by worms on fine, algae-rich particles strongly decreases the abundance and richness of all three domains. In these deeper layers, bacterial and eukaryotic network connectivity decreases, while percentages of clades involved in degradation of refractory organic matter, oxidative nitrogen, and sulfur cycling increase. Our findings reveal macrofaunal activity as the key driver of biological community structure and functioning, that in turn influence carbon cycling in intertidal sands below the mainly physically controlled surface layer.
Collapse
Affiliation(s)
| | - Christof Meile
- Department of Marine Sciences, University of Georgia, 325 Sanford Drive, Athens, GA 30602, USA
| | | | - Damian Bölsterli
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | | | - Niroshan Gajendra
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Nathalie Dubois
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Sonneggstrasse 5, 8092 Zürich, Switzerland
| | - Stefano M Bernasconi
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Sonneggstrasse 5, 8092 Zürich, Switzerland
| | - Mark A Lever
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| |
Collapse
|
10
|
Pan X, Zhang S, Li T, Ouyang J, Gong G, Wang G, Xu X, Pu Y, Long L, Jia Y. Response of microbiomes with different abundances to removal of metal fractions by soil washing. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113862. [PMID: 35835071 DOI: 10.1016/j.ecoenv.2022.113862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Toxic metal contamination causes a great threat to soil ecosystem and human health. Soil washing is a fast practice for removing metals, but its influences on microbial diversity and the stability of soil ecosystem remain unknown. In this study, ethylenediaminetetraacetic acid (EDTA), citric acid (CA), and fermented pineapple peel residue (FPP) were used as representatives of chelates, low molecular organic acids and biological materials to wash Pb-polluted soils, and their impacts on microbial community were investigated. Washing with these agents effectively removed Pb, but altered microbial community structure. After washing with EDTA, CA, and FPP, 3-8 bacterial phyla and 1 fungal phylum greatly increased, while 7-20 bacterial and 0-6 fungal phyla severely decreased or even disappeared. The alterations of different microbiomes were closely related to soil metal fractions. The labile metal fraction had negative effects on most bacteria and fungi, but also showed positive influences on Actinobacteria, Patescibacteria, and Fusobacteria. The moderately stable and stable fractions were nontoxic to the most microbes, but still harmful to Patescibacteria and Deinococcus-Thermus. These findings provide new insights for the effects of soil washing remediation and toxicity of metal fractions on the microbiomes with different abundance.
Collapse
Affiliation(s)
- Xiaomei Pan
- College of Environmental Sciences, Sichuan Agricultural University, Wenjiang 611130, China; Chengdu Agricultural College, Wenjiang 611130, China
| | - Shirong Zhang
- College of Environmental Sciences, Sichuan Agricultural University, Wenjiang 611130, China; Sichuan Provincial Key Laboratory of Soil Environmental Protection, Wenjiang 611130, China.
| | - Ting Li
- College of Resources, Sichuan Agricultural University, Wenjiang 611130, China
| | - Jinyi Ouyang
- College of Resources, Sichuan Agricultural University, Wenjiang 611130, China
| | - Guoshu Gong
- College of Agronomy, Sichuan Agricultural University, Wenjiang 611130, China
| | - Guiyin Wang
- College of Environmental Sciences, Sichuan Agricultural University, Wenjiang 611130, China; Sichuan Provincial Key Laboratory of Soil Environmental Protection, Wenjiang 611130, China
| | - Xiaoxun Xu
- College of Environmental Sciences, Sichuan Agricultural University, Wenjiang 611130, China; Sichuan Provincial Key Laboratory of Soil Environmental Protection, Wenjiang 611130, China
| | - Yulin Pu
- College of Resources, Sichuan Agricultural University, Wenjiang 611130, China
| | - Lulu Long
- College of Environmental Sciences, Sichuan Agricultural University, Wenjiang 611130, China
| | - Yongxia Jia
- College of Environmental Sciences, Sichuan Agricultural University, Wenjiang 611130, China
| |
Collapse
|
11
|
Chen S, Yang D, Wang Q, Huang X, Ren H, Xu K. Study on the advanced nitrogen removal under low temperature by biofilm on weak magnetic carriers. BIORESOURCE TECHNOLOGY 2022; 360:127580. [PMID: 35798170 DOI: 10.1016/j.biortech.2022.127580] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/26/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
The advanced nitrogen removal under low temperature is inhibited because of reduction of the microbial activity. Packed bed reactors filled with different magnetic carriers (0, 0.3, 0.6, 0.9 mT) were constructed to enhance advanced denitrification under low temperature (5 ℃). Results showed that 0.3 and 0.9 mT carriers significantly improved denitrification, indicating the "window" effect. Total nitrogen removals were increased by 6.96% and 8.25%, and NO2- accumulation decreased by 25.70% and 13.90% in 0.3 and 0.9 mT reactors, respectively. Analysis of enzyme activity and electron transport chain showed that 0.3 mT carrier mainly increased NIR activity by improving compound III and cytC abundance while 0.9 mT carrier mainly increased NAR activity by improving compound I and NADH abundance, indicating different pathways. Similar microbial community in 0.3 and 0.9 mT reactors were revealed. Overall, weak magnetic carriers can be used to enhance advanced nitrogen removal under low temperature.
Collapse
Affiliation(s)
- Sien Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Dongli Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qingxin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xueying Huang
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ke Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| |
Collapse
|
12
|
Pavlova ON, Izosimova ON, Chernitsyna SM, Ivanov VG, Pogodaeva TV, Khabuev AV, Gorshkov AG, Zemskaya TI. Anaerobic oxidation of petroleum hydrocarbons in enrichment cultures from sediments of the Gorevoy Utes natural oil seep under methanogenic and sulfate-reducing conditions. MICROBIAL ECOLOGY 2022; 83:899-915. [PMID: 34255112 DOI: 10.1007/s00248-021-01802-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
This article presents the first experimental data on the ability of microbial communities from sediments of the Gorevoy Utes natural oil seep to degrade petroleum hydrocarbons under anaerobic conditions. Like in marine ecosystems associated with oil discharge, available electron acceptors, in particular sulfate ions, affect the composition of the microbial community and the degree of hydrocarbon conversion. The cultivation of the surface sediments under sulfate-reducing conditions led to the formation of a more diverse bacterial community and greater loss of n-alkanes (28%) in comparison to methanogenic conditions (6%). Microbial communities of both surface and deep sediments are more oriented to degrade polycyclic aromatic hydrocarbons (PAHs), to which the degree of the PAH conversion testifies (up to 46%) irrespective of the present electron acceptors. Microorganisms with the uncultured closest homologues from thermal habitats, sediments of mud volcanoes, and environments contaminated with hydrocarbons mainly represented microbial communities of enrichment cultures. The members of the phyla Firmicutes, Chloroflexi, and Caldiserica (OP5), as well as the class Deltaproteobacteria and Methanomicrobia, were mostly found in enrichment cultures. The influence of gas-saturated fluids may be responsible for the presence in the bacterial 16S rRNA gene libraries of the sequences of "rare taxa": Planctomycetes, Ca. Atribacteria (OP9), Ca. Armatimonadetes (OP10), Ca. Latescibacteria (WS3), Ca. division (AC1), Ca. division (OP11), and Ca. Parcubacteria (OD1), which can be involved in hydrocarbon oxidation.
Collapse
Affiliation(s)
- O N Pavlova
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia.
| | - O N Izosimova
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - S M Chernitsyna
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - V G Ivanov
- Laboratory of Hydrology and Hydrophysics, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T V Pogodaeva
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A V Khabuev
- Laboratory of Lake Baikal Geology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A G Gorshkov
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T I Zemskaya
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| |
Collapse
|
13
|
Williams TJ, Allen MA, Panwar P, Cavicchioli R. Into the darkness: The ecologies of novel 'microbial dark matter' phyla in an Antarctic lake. Environ Microbiol 2022; 24:2576-2603. [PMID: 35466505 PMCID: PMC9324843 DOI: 10.1111/1462-2920.16026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022]
Abstract
Uncultivated microbial clades ("microbial dark matter") are inferred to play important, but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome-assembled genomes (MAGs; 88-100% complete) were generated for four "dark matter" phyla: six MAGs from Candidatus Auribacterota (= Aureabacteria, SURF-CP-2), inferred to be hydrogen- and sulfide-producing fermentative heterotrophs, with individual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili; one MAG (100% complete) from Candidatus Hinthialibacterota (= OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g., sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili; three MAGs from Candidatus Electryoneota (= AABM5-125-24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes; two MAGs from Candidatus Lernaellota (= FEN-1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88-100% identity) suggests these "dark matter" phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautrophic CO2 fixation in diverse global environments. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences UNSW Sydney, Sydney, New South Wales, 2052, Australia
| |
Collapse
|
14
|
Kaluzhnaya OV, Itskovich VB. Features of Diversity of Polyketide Synthase Genes in the Community of Freshwater Sponge Baikalospongia fungiformis. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422030061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Fiard M, Cuny P, Sylvi L, Hubas C, Jézéquel R, Lamy D, Walcker R, El Houssainy A, Heimbürger-Boavida LE, Robinet T, Bihannic I, Gilbert F, Michaud E, Dirberg G, Militon C. Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150667. [PMID: 34599952 DOI: 10.1016/j.scitotenv.2021.150667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.
Collapse
Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cédric Hubas
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Dominique Lamy
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France; Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), Sorbonne Université, Univ Paris Est Créteil, IRD, CNRS, INRA, 4 place Jussieu, 75005 Paris, France.
| | - Romain Walcker
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Amonda El Houssainy
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | | | - Tony Robinet
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Franck Gilbert
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| |
Collapse
|
16
|
Govindarajan A, Crum M, Adolacion J, Kiaghadi A, Acuña-Gonzalez E, Rifai HS, Willson RC. Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey. MARINE POLLUTION BULLETIN 2022; 175:113359. [PMID: 35124375 DOI: 10.1016/j.marpolbul.2022.113359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/26/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.
Collapse
Affiliation(s)
| | - Mary Crum
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Jay Adolacion
- School of Engineering and Science, Tecnológico de Monterrey, Monterrey, Mexico
| | - Amin Kiaghadi
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA
| | - Edgar Acuña-Gonzalez
- School of Medicine and Health Sciences, Tecnológico de Monterrey, Monterrey, Mexico
| | - Hanadi S Rifai
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA.
| | - Richard C Willson
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| |
Collapse
|
17
|
Martínez-Pérez C, Greening C, Bay SK, Lappan RJ, Zhao Z, De Corte D, Hulbe C, Ohneiser C, Stevens C, Thomson B, Stepanauskas R, González JM, Logares R, Herndl GJ, Morales SE, Baltar F. Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf. Nat Commun 2022; 13:117. [PMID: 35013291 PMCID: PMC8748734 DOI: 10.1038/s41467-021-27769-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
Throughout coastal Antarctica, ice shelves separate oceanic waters from sunlight by hundreds of meters of ice. Historical studies have detected activity of nitrifying microorganisms in oceanic cavities below permanent ice shelves. However, little is known about the microbial composition and pathways that mediate these activities. In this study, we profiled the microbial communities beneath the Ross Ice Shelf using a multi-omics approach. Overall, beneath-shelf microorganisms are of comparable abundance and diversity, though distinct composition, relative to those in the open meso- and bathypelagic ocean. Production of new organic carbon is likely driven by aerobic lithoautotrophic archaea and bacteria that can use ammonium, nitrite, and sulfur compounds as electron donors. Also enriched were aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates, likely derived from in situ fixed carbon and potentially refractory organic matter laterally advected by the below-shelf waters. Altogether, these findings uncover a taxonomically distinct microbial community potentially adapted to a highly oligotrophic marine environment and suggest that ocean cavity waters are primarily chemosynthetically-driven systems.
Collapse
Affiliation(s)
- Clara Martínez-Pérez
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 8093, Zurich, Switzerland
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, 3800, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, 3800, Australia
| | - Rachael J Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Daniele De Corte
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Hulbe
- School of Surveying, University of Otago, Dunedin, New Zealand
| | | | - Craig Stevens
- National Institute of Water and Atmospheric Research, Greta Point, Wellington, 6021, New Zealand
- Department of Physics, University of Auckland, Auckland, New Zealand
| | - Blair Thomson
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
| | | | - José M González
- Department of Microbiology, University of La Laguna, ES-38200, La Laguna, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, PO Box 59, 1790, AB Den Burg, The Netherlands
- Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
18
|
Flood BE, Louw DC, Van der Plas AK, Bailey JV. Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes. PLoS One 2021; 16:e0258124. [PMID: 34818329 PMCID: PMC8612568 DOI: 10.1371/journal.pone.0258124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.
Collapse
Affiliation(s)
- Beverly E. Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail:
| | - Deon C. Louw
- National Marine Information and Research Centre, Swakopmund, Namibia
| | | | - Jake V. Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
| |
Collapse
|
19
|
Demko AM, Patin NV, Jensen PR. Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques. Environ Microbiol 2021; 23:6859-6875. [PMID: 34636122 DOI: 10.1111/1462-2920.15798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 09/28/2021] [Indexed: 01/04/2023]
Abstract
The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.
Collapse
Affiliation(s)
- Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
20
|
Grodnitskaya ID, Kuznetsova GV, Pashkeeva OE, Antonov GI. Features of the Formation of Microbiomes in Two Types of Soils under Pine Provenance Trials of Pinus sibirica Du Tour and Pinus koraiensis Siebold et Zucc. BIOL BULL+ 2021. [DOI: 10.1134/s1062359021030067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
21
|
El-Naggar NEA, Hamouda RA, Abuelmagd MA, Abdelgalil SA. Bioprocess development for biosorption of cobalt ions and Congo red from aquatic mixture using Enteromorpha intestinalis biomass as sustainable biosorbent. Sci Rep 2021; 11:14953. [PMID: 34294748 PMCID: PMC8298401 DOI: 10.1038/s41598-021-94026-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
Because of the increased amount of cobalt and Congo red dye effluents attributable to the industrial operations, the capacity of Enteromorpha intestinalis biomass as a sustainable source to achieve significant biosorption percent for both pollutants from dual solution was assessed. A fifty batch FCCCD experiments for biosorption of cobalt ions and Congo red dye were performed. The complete removal of Congo red dye was obtained at 36th run using an initial pH value of 10, 1.0 g/L of Enteromorpha intestinalis biomass, 100 and 200 mg/L of Congo red and cobalt for a 20-min incubation time. Meanwhile, a cobalt removal percent of 85.22 was obtained at 35th run using a neutral pH of 7.0, 3.0 g/L of algal biomass, 150 and 120 mg/L of Congo red, and cobalt for a 60-min incubation time. For further illustration and to interpret how the biosorption mechanism was performed, FTIR analysis was conducted to inspect the role of each active group in the biosorption process, it can be inferred that -OH, C-H, C=O, O-SO3- and C-O-C groups were mainly responsible for Co2+ adsorption of from aqueous dual solution. Also, scan electron microscope revealed the appearance of new shiny particles biosorbed on E. intestinalis surface after the biosorption process. EDS analysis proved the presence of Co2+ on the algal surface after the biosorption process.
Collapse
Affiliation(s)
- Noura El-Ahmady El-Naggar
- Department of Bioprocess Development, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg El‑Arab City, 21934, Alexandria, Egypt.
| | - Ragaa A Hamouda
- Department of Biology, College of Sciences and Arts Khulais,, University of Jeddah, Jeddah, Saudi Arabia
- Microbial Biotechnology Department, Genetic Engineering and Biotechnology, Research Institute, University of Sadat City, El Sadat City, Egypt
| | | | - Soad A Abdelgalil
- Department of Bioprocess Development, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg El‑Arab City, 21934, Alexandria, Egypt
| |
Collapse
|
22
|
Oyetibo GO, Ige OO, Obinani PK, Amund OO. Ecological risk potentials of petroleum hydrocarbons and heavy metals shape the bacterial communities of marine hydrosphere at Atlantic Ocean, Atlas Cove, Nigeria. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112563. [PMID: 33852998 DOI: 10.1016/j.jenvman.2021.112563] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/26/2021] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
Trans-Atlantic voyage of petroleum often leads to marine pollution with petroleum hydrocarbons (PHs) and heavy metals (HMs) that defines structures of autochthonous bacteria in the hydrosphere. Bacterial taxa of marine sediments exposed to petroleum transport activities were profiled using 16S rDNA metagenomics and correlated with the geochemistry to establish their impact on the microbiome. The physico-chemistry of the marine systems revealed varied degrees of contamination with PHs and HMs exceeding recommended threshold for aquatic life. Ecological risk assessment based on organic carbon of the sediment established phenanthrene, anthracene, and pyrene posed high risks (index risk quotient >32) to marine life. The most dominant phylum of the 44 bacterial phyla in the marine-sphere was Proteobacteria with relative abundance of 45-77% in the sampling locations. Relative dominance of Proteobacteria in the sediments spanned Gammaproteobacteria (17-25%), Deltaproteobacteria (12-20%), and Alphaproteobacteria (7-14%). Whereas, more operational taxonomic units (OTUs) belonging to Epsilonproteobacteria (19 ± 2.4%) were found in estuarine sediment unlike < 0.5% relative abundances obtained from oceanic sediments. Sulfurimonas apparently dominated the bacterial genera with up to 2.16 ± 0.19% abundance in oceanic sediments. Canonical correspondence analysis revealed that PHs shaped the structure of bacterial OTUs in oceanic sediments where petroleum loading/offloading occurs unlike in some kilometres a yonder where HMs correlated with the bacteria structure. The dominant bacteria might possibly pivotal to ecophysiologies of hydrocarbon contaminated marine environment, and would be pertinent to biotechnological applications for possible bioremediation campaign.
Collapse
Affiliation(s)
- Ganiyu O Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria.
| | - Oluwatobi O Ige
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria
| | - Peace K Obinani
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria
| | - Olukayode O Amund
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria
| |
Collapse
|
23
|
Navarrete-Euan H, Rodríguez-Escamilla Z, Pérez-Rueda E, Escalante-Herrera K, Martínez-Núñez MA. Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan. Microorganisms 2021; 9:microorganisms9040877. [PMID: 33923859 PMCID: PMC8073884 DOI: 10.3390/microorganisms9040877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 12/27/2022] Open
Abstract
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.
Collapse
Affiliation(s)
- Herón Navarrete-Euan
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Zuemy Rodríguez-Escamilla
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Unidad Académica Yucatán, Mérida, Yucatán 97302, Mexico;
| | - Karla Escalante-Herrera
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
- Correspondence: ; Tel.: +52-999-3410860 (ext. 7631)
| |
Collapse
|
24
|
Vogel MA, Mason OU, Miller TE. Composition of seagrass phyllosphere microbial communities suggests rapid environmental regulation of community structure. FEMS Microbiol Ecol 2021; 97:6119907. [PMID: 33493257 DOI: 10.1093/femsec/fiab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/22/2021] [Indexed: 01/04/2023] Open
Abstract
Recent studies have revealed that seagrass blade surfaces, also known as the phyllosphere, are rich habitats for microbes; however, the primary drivers of composition and structure in these microbial communities are largely unknown. This study utilized a reciprocal transplant approach between two sites with different environmental conditions combined with 16S rRNA gene sequencing (iTag) to examine the relative influence of environmental conditions and host plant on phyllosphere community composition of the seagrass Thalassia testudinum. After 30 days, identity of phyllosphere microbial community members was more similar within the transplant sites than between despite differences in the source of host plant. Additionally, the diversity and evenness of these communities was significantly different between the two sites. These results indicated that local environmental conditions can be a primary driver in structuring seagrass phyllosphere microbial communities over relatively short time scales. Composition of microbial community members in this study also deviated from those in previous seagrass phyllosphere studies with a higher representation of candidate bacterial phyla and archaea than previously observed. The capacity for seagrass phyllosphere microbial communities to shift dramatically with environmental conditions, including ecosystem perturbations, could significantly affect seagrass-microbe interactions in ways that may influence the health of the seagrass host.
Collapse
Affiliation(s)
- Margaret A Vogel
- Florida State University, Department of Biological Science, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Olivia U Mason
- Florida State University, Department of Earth, Ocean, and Atmospheric Science, 1011 Academic Way, Tallahassee, FL 32306, USA
| | - Thomas E Miller
- Florida State University, Department of Biological Science, 319 Stadium Drive, Tallahassee, FL 32306, USA
| |
Collapse
|
25
|
Dell'Anno F, Rastelli E, Tangherlini M, Corinaldesi C, Sansone C, Brunet C, Balzano S, Ianora A, Musco L, Montereali MR, Dell'Anno A. Highly Contaminated Marine Sediments Can Host Rare Bacterial Taxa Potentially Useful for Bioremediation. Front Microbiol 2021; 12:584850. [PMID: 33732217 PMCID: PMC7956957 DOI: 10.3389/fmicb.2021.584850] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/02/2021] [Indexed: 01/04/2023] Open
Abstract
Coastal areas impacted by high anthropogenic pressures typically display sediment contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs). Microbial-based bioremediation represents a promising strategy for sediment reclamation, yet it frequently fails due to poor knowledge of the diversity and dynamics of the autochthonous microbial assemblages and to the inhibition of the target microbes in the contaminated matrix. In the present study, we used an integrated approach including a detailed environmental characterization, high-throughput sequencing and culturing to identify autochthonous bacteria with bioremediation potential in the sediments of Bagnoli-Coroglio (Gulf of Naples, Mediterranean Sea), a coastal area highly contaminated by PAHs, aliphatic hydrocarbons and HMs. The analysis of the benthic prokaryotic diversity showed that the distribution of the dominant taxon (Gammaproteobacteria) was mainly influenced by PAHs, As, and Cd concentrations. The other abundant taxa (including Alphaproteobacteria, Deltaproteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, NB1-j, Desulfobacterota, and Myxococcota) were mainly driven by sediment grain size and by Cu and Cr concentrations, while the rare taxa (i.e., each contributing <1%) by As and aliphatic hydrocarbons concentrations and by sediment redox potential. These results suggest a differential response of bacterial taxa to environmental features and chemical contamination and those different bacterial groups may be inhibited or promoted by different contaminants. This hypothesis was confirmed by culturing and isolating 80 bacterial strains using media highly enriched in PAHs, only nine of which were contextually resistant to high HM concentrations. Such resistant isolates represented novel Gammaproteobacteria strains affiliated to Vibrio, Pseudoalteromonas, and Agarivorans, which were only scarcely represented in their original assemblages. These findings suggest that rare but culturable bacterial strains resistant/tolerant to high levels of mixed contaminants can be promising candidates useful for the reclamation by bioaugmentation strategies of marine sediments that are highly contaminated with PAHs and HMs.
Collapse
Affiliation(s)
| | | | | | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
| | | | | | | | | | - Luigi Musco
- Stazione Zoologica Anton Dohrn, Naples, Italy.,Laboratory of Marine Biology and Zoology, DiSTeBA, University of Salento, Lecce, Italy
| | - Maria Rita Montereali
- ENEA - Agenzia per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile, Rome, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| |
Collapse
|
26
|
Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes. Microorganisms 2020; 8:microorganisms8101592. [PMID: 33081076 PMCID: PMC7602701 DOI: 10.3390/microorganisms8101592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years old, in two Mexican communities with contrasting lifestyles, i.e., “Westernized” (México City, n = 13) and “non-Westernized” (Me’phaa indigenous group, n = 29), in order to characterize and compare their GM. The main differences between these two communities were in bacteria associated with different types of diets (high animal protein and refined sugars vs. high fiber food, respectively). In addition, the GM of Me’phaa children showed higher total diversity and the presence of exclusive phyla, such as Deinococcus-Thermus, Chloroflexi, Elusimicrobia, Acidobacteria, and Fibrobacteres. In contrast, the children from México City showed less diversity and the presence of Saccharibacteria phylum, which was associated with the degradation of sugar compounds and was not present in the samples from Me’phaa children. This comparison provided further knowledge of the selective pressures affecting microbial ecosystemic composition over the course of human evolution and the potential consequences of pathophysiological states correlated with Westernization lifestyles.
Collapse
|
27
|
Seward J, Carson MA, Lamit LJ, Basiliko N, Yavitt JB, Lilleskov E, Schadt CW, Smith DS, Mclaughlin J, Mykytczuk N, Willims-Johnson S, Roulet N, Moore T, Harris L, Bräuer S. Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient. MICROBIAL ECOLOGY 2020; 80:593-602. [PMID: 32388577 DOI: 10.1007/s00248-020-01510-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/30/2020] [Indexed: 05/20/2023]
Abstract
Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.
Collapse
Affiliation(s)
- James Seward
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608-2026, USA.
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada.
| | - Michael A Carson
- Department of Renewable Resources, Earth Sciences Building, University of Alberta, 116 St. and 85 Ave., Edmonton, Alberta, T6G 2R3, Canada
| | - L J Lamit
- Department of Biology, Syracuse University, Syracuse, NY, USA
| | - Nathan Basiliko
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, 14853, USA
| | - Erik Lilleskov
- USDA Forest Service, Northern Research Station, 410 MacInnes Dr, Houghton, MI, 49931, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6038, USA
| | - Dave Solance Smith
- Department of Biology, California State University, San Bernardino, CA, 92407, USA
| | - Jim Mclaughlin
- Ontario Forest Research Institute, Sault Ste. Marie, ON, Canada
| | - Nadia Mykytczuk
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada
| | - Shanay Willims-Johnson
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada
| | - Nigel Roulet
- Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Tim Moore
- Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Lorna Harris
- Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Suzanna Bräuer
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608-2026, USA
| |
Collapse
|
28
|
Cullings K, Stott MB, Marinkovich N, DeSimone J, Bhardwaj S. Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert. Microbiologyopen 2020; 9:e1062. [PMID: 32478485 PMCID: PMC7424252 DOI: 10.1002/mbo3.1062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.
Collapse
Affiliation(s)
- Ken Cullings
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Julia DeSimone
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Shilpa Bhardwaj
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| |
Collapse
|
29
|
He P, Xie L, Zhang X, Li J, Lin X, Pu X, Yuan C, Tian Z, Li J. Microbial Diversity and Metabolic Potential in the Stratified Sansha Yongle Blue Hole in the South China Sea. Sci Rep 2020; 10:5949. [PMID: 32249806 PMCID: PMC7136235 DOI: 10.1038/s41598-020-62411-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/11/2020] [Indexed: 01/08/2023] Open
Abstract
The Sansha Yongle Blue Hole is the world’s deepest (301 m) underwater cave and has a sharp redox gradient, with oligotrophic, anoxic, and sulfidic bottom seawater. In order to discover the microbial communities and their special biogeochemical pathways in the blue hole, we analyzed the 16S ribosomal RNA amplicons and metagenomes of microbials from seawater depths with prominent physical, chemical, and biological features. Redundancy analysis showed that dissolved oxygen was the most important factor affecting the microbial assemblages of the blue hole and surrounding open sea waters, and significantly explained 44.7% of the total variation, followed by silicate, temperature, sulfide, ammonium, methane, nitrous oxide, nitrate, dissolved organic carbon, salinity, particulate organic carbon, and chlorophyll a. We identified a bloom of Alteromonas (34.9%) at the primary nitrite maximum occurring in close proximity to the chlorophyll a peak in the blue hole. Genomic potential for nitrate reduction of Alteromonas might contribute to this maximum under oxygen decrease. Genes that would allow for aerobic ammonium oxidation, complete denitrification, and sulfur-oxidization were enriched at nitrate/nitrite-sulfide transition zone (90 and 100 m) of the blue hole, but not anammox pathways. Moreover, γ-Proteobacterial clade SUP05, ε-Proteobacterial genera Sulfurimonas and Arcobacter, and Chlorobi harbored genes for sulfur-driven denitrification process that mediated nitrogen loss and sulfide removal. In the anoxic bottom seawater (100-300 m), high levels of sulfate reducers and dissimilatory sulfite reductase gene (dsrA) potentially created a sulfidic zone of ~200 m thickness. Our findings suggest that in the oligotrophic Sansha Yongle Blue Hole, O2 deficiency promotes nitrogen- and sulfur-cycling processes mediated by metabolically versatile microbials.
Collapse
Affiliation(s)
- Peiqing He
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China. .,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China. .,Key Laboratory of Natural Products of Qingdao, Qingdao, 266061, China.
| | - Linping Xie
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xuelei Zhang
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Jiang Li
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Key Laboratory of Natural Products of Qingdao, Qingdao, 266061, China
| | - Xuezheng Lin
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Key Laboratory of Natural Products of Qingdao, Qingdao, 266061, China
| | - Xinming Pu
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Chao Yuan
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Ziwen Tian
- Research Center for Islands and Coastal Zone, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China
| | - Jie Li
- Marine Engineering Environment and Geomatic Center, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China
| |
Collapse
|
30
|
Chen ML, Becraft ED, Pachiadaki M, Brown JM, Jarett JK, Gasol JM, Ravin NV, Moser DP, Nunoura T, Herndl GJ, Woyke T, Stepanauskas R. Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. Front Microbiol 2020; 11:376. [PMID: 32226422 PMCID: PMC7081726 DOI: 10.3389/fmicb.2020.00376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/20/2020] [Indexed: 12/31/2022] Open
Abstract
Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.
Collapse
Affiliation(s)
- Michael L Chen
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, Williams College, Williamstown, MA, United States
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, University of North Alabama, Florence, AL, United States
| | - Maria Pachiadaki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Jessica K Jarett
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Josep M Gasol
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.,Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | | |
Collapse
|
31
|
Reis AC, Kolvenbach BA, Chami M, Gales L, Egas C, Corvini PFX, Nunes OC. Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. BMC Genomics 2019; 20:885. [PMID: 31752666 PMCID: PMC6868719 DOI: 10.1186/s12864-019-6206-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/21/2019] [Indexed: 02/01/2023] Open
Abstract
Background Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified. Results Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements. Conclusions Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.
Collapse
Affiliation(s)
- Ana C Reis
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.,Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Mohamed Chami
- BioEM lab, C-Cina, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Luís Gales
- Instituto de Investigação e Inovação em Saúde - i3S, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Biologia Molecular e Celular - IBMC, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar - ICBAS, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Faculty of Medicine, Rua Larga, Pólo I, 3004-504, Coimbra, Portugal
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Olga C Nunes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
| |
Collapse
|
32
|
Spatial Variations of Bacterial Communities of an Anaerobic Lagoon-Type Biodigester Fed with Dairy Manure. Processes (Basel) 2019. [DOI: 10.3390/pr7070408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Anaerobic digestion technology is being widely employed for sustainable management of organic wastes generated in animal farms, industries, etc. Nevertheless, biodigester microbiome is still considered a “black box” because it is regulated by different physico-chemical and operational factors. In this study, the bacterial diversity and composition in different sites of a full-scale lagoon type biodigester (23,000 m3) fed with dairy manure, viz., the influent, beginning, middle, final and effluent were analyzed. The biodigester registered a total of 1445 OTUs, which demonstrated the complex microbial ecosystem in it. Of them, only six OTUs were shared among all the different sampling points. The most abundant phyla belonged to Firmicutes, Proteobacteria, Latescibacteria and Thermotogae. The Simpson and Shannon index showed that the highest microbial diversity was observed in the beginning point of the biodigester, meanwhile, the lowest diversity was recorded in the middle. Based on the UniFrac distances, microbial communities with high similarity were recorded in the middle and final of the biodigester. It can be clearly observed that bacterial communities varied at the different points of the biodigester. However, based on metagenome predictions using PICRUSt, it was found that independent of the differences in taxonomy and location, bacterial communities maintained similar metabolic functions.
Collapse
|
33
|
Bio-engineering of bacterial microcompartments: a mini review. Biochem Soc Trans 2019; 47:765-777. [DOI: 10.1042/bst20170564] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/09/2019] [Accepted: 05/22/2019] [Indexed: 12/30/2022]
Abstract
AbstractBacterial microcompartments (BMCs) are protein-bound prokaryotic organelles, discovered in cyanobacteria more than 60 years ago. Functionally similar to eukaryotic cellular organelles, BMCs compartment metabolic activities in the cytoplasm, foremost to increase local enzyme concentration and prevent toxic intermediates from damaging the cytosolic content. Advanced knowledge of the functional and structural properties of multiple types of BMCs, particularly over the last 10 years, have highlighted design principles of microcompartments. This has prompted new research into their potential to function as programmable synthetic nano-bioreactors and novel bio-materials with biotechnological and medical applications. Moreover, due to the involvement of microcompartments in bacterial pathogenesis and human health, BMCs have begun to gain attention as potential novel drug targets. This mini-review gives an overview of important synthetic biology developments in the bioengineering of BMCs and a perspective on future directions in the field.
Collapse
|
34
|
Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities. Appl Environ Microbiol 2019; 85:AEM.00110-19. [PMID: 30902854 DOI: 10.1128/aem.00110-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
Recent experimental and bioinformatic advances enable the recovery of genomes belonging to yet-uncultured microbial lineages directly from environmental samples. Here, we report on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences. Analysis of LCP-89 genomes recovered from Zodletone Spring, an anoxic spring in Oklahoma, predicts slow-growing, rod-shaped organisms. LCP-89 genomes contain genes for cell wall lipopolysaccharide (LPS) production but lack the entire machinery for peptidoglycan biosynthesis, suggesting an atypical cell wall structure. The genomes, however, encode S-layer homology domain-containing proteins, as well as machinery for the biosynthesis of CMP-legionaminate, inferring the possession of an S-layer glycoprotein. A nearly complete chemotaxis machinery coupled to the absence of flagellar synthesis and assembly genes argues for the utilization of alternative types of motility. A strict anaerobic lifestyle is predicted, with dual respiratory (nitrite ammonification) and fermentative capacities. Predicted substrates include a wide range of sugars and sugar alcohols and a few amino acids. The capability of rhamnose metabolism is confirmed by the identification of bacterial microcompartment genes to sequester the toxic intermediates generated. Comparative genomic analysis identified differences in oxygen sensitivities, respiratory capabilities, substrate utilization preferences, and fermentation end products between LCP-89 genomes and those belonging to its four sister phyla (Calditrichota, SM32-31, AABM5-125-24, and KSB1) within the broader FCB (Fibrobacteres-Chlorobi-Bacteroidetes) superphylum. Our results provide a detailed characterization of members of the candidate division LCP-89 and highlight the importance of reconciling 16S rRNA-based and genome-based phylogenies.IMPORTANCE Our understanding of the metabolic capacities, physiological preferences, and ecological roles of yet-uncultured microbial phyla is expanding rapidly. Two distinct approaches are currently being utilized for characterizing microbial communities in nature: amplicon-based 16S rRNA gene surveys for community characterization and metagenomics/single-cell genomics for detailed metabolic reconstruction. The occurrence of multiple yet-uncultured bacterial phyla has been documented using 16S rRNA surveys, and obtaining genome representatives of these yet-uncultured lineages is critical to our understanding of the role of yet-uncultured organisms in nature. This study provides a genomics-based analysis highlighting the structural features and metabolic capacities of a yet-uncultured bacterial phylum (LCP-89) previously identified in 16S rRNA surveys for which no prior genomes have been described. Our analysis identifies several interesting structural features for members of this phylum, e.g., lack of peptidoglycan biosynthetic machinery and the ability to form bacterial microcompartments. Predicted metabolic capabilities include degradation of a wide range of sugars, anaerobic respiratory capacity, and fermentative capacities. In addition to the detailed structural and metabolic analysis provided for candidate division LCP-89, this effort represents an additional step toward a unified scheme for microbial taxonomy by reconciling 16S rRNA gene-based and genomics-based taxonomic outlines.
Collapse
|
35
|
Tyler HL. Bacterial community composition under long‐term reduced tillage and no till management. J Appl Microbiol 2019; 126:1797-1807. [DOI: 10.1111/jam.14267] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/13/2019] [Accepted: 03/25/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Heather L. Tyler
- Crop Production Systems Research Unit USDA Agricultural Research Service Stoneville MS USA
| |
Collapse
|
36
|
Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media - A review. J Adv Res 2019; 19:15-27. [PMID: 31341666 PMCID: PMC6630032 DOI: 10.1016/j.jare.2019.04.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/22/2022] Open
Abstract
The plant microbiome culturomics is substantially lagging behind the human microbiome. Conventional chemically-synthetic culture media recover < 10% of plant-associated microbiota. Plant-based culture media (PCM) are introduced as a novel tool for plant microbiome culturomics. PCM extended the microbiota culturability to recover unculturable bacterial taxa. Streamlined- and large-genomes conspicuously contribute to the dilemma of unculturability.
Improving cultivability of a wider range of bacterial and archaeal community members, living natively in natural environments and within plants, is a prerequisite to better understanding plant-microbiota interactions and their functions in such very complex systems. Sequencing, assembling, and annotation of pure microbial strain genomes provide higher quality data compared to environmental metagenome analyses, and can substantially improve gene and protein database information. Despite the comprehensive knowledge which already was gained using metagenomic and metatranscriptomic methods, there still exists a big gap in understanding in vivo microbial gene functioning in planta, since many differentially expressed genes or gene families are not yet annotated. Here, the progress in culturing procedures for plant microbiota depending on plant-based culture media, and their proficiency in obtaining single prokaryotic isolates of novel and rapidly increasing candidate phyla are reviewed. As well, the great success of culturomics of the human microbiota is considered with the main objective of encouraging microbiologists to continue minimizing the gap between the microbial richness in nature and the number of species in culture, for the benefit of both basic and applied microbiology. The clear message to fellow plant microbiologists is to apply plant-tailored culturomic techniques that might open up novel procedures to obtain not-yet-cultured organisms and extend the known plant microbiota repertoire to unprecedented levels.
Collapse
|
37
|
Sutcliffe B, Hose GC, Harford AJ, Midgley DJ, Greenfield P, Paulsen IT, Chariton AA. Microbial communities are sensitive indicators for freshwater sediment copper contamination. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:1028-1038. [PMID: 30823331 DOI: 10.1016/j.envpol.2019.01.104] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 01/20/2019] [Accepted: 01/26/2019] [Indexed: 06/09/2023]
Abstract
Anthropogenic activities, such as mining and agriculture, have resulted in many freshwater systems having elevated concentrations of copper. Despite the prevalence of this contamination, and the vital ecological function of prokaryotes, just three studies have investigated prokaryote community responses to copper concentration in freshwater sediments. To address this, the current study investigated these communities in outdoor mesocosms spiked with varying copper concentrations. We profiled the prokaryotic communities at the taxonomic level, using next-generation high-throughput sequencing techniques, as well as their function, using baiting with leaf analogues, and Biolog Ecoplates for community-level physiological profiling. Sediments containing just 46 mg kg-1 of copper, had distinctly different microbial communities compared with controls, as determined by both DNA and RNA 16S ribosomal RNA gene (rRNA) profiling. In addition to this, sediment communities displayed a greatly reduced utilisation of carbon substrates under elevated copper, while the communities recruited onto leaf analogues were also disparate from those of control ponds. Given the vital role of prokaryotes in ecosystem processes, including carbon cycling, these changes are potentially of great ecological relevance, and are seen to occur well below the 'low risk' sediment quality guideline values (SQGV) used by regulatory bodies internationally.
Collapse
Affiliation(s)
- B Sutcliffe
- Macquarie University, Sydney, New South Wales, 2109, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia.
| | - G C Hose
- Macquarie University, Sydney, New South Wales, 2109, Australia
| | - A J Harford
- Supervising Scientist Branch, Department of the Environment and Energy, Darwin, NT, Australia
| | - D J Midgley
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia
| | - P Greenfield
- Macquarie University, Sydney, New South Wales, 2109, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia
| | - I T Paulsen
- Macquarie University, Sydney, New South Wales, 2109, Australia
| | - A A Chariton
- Macquarie University, Sydney, New South Wales, 2109, Australia.
| |
Collapse
|
38
|
Gong B, Huang H, Peng C, Wang J, Ma J, Liu X, Ouyang S, Huang SL, Wu H. The microbiomic and environmental analysis of sediments in the Indo-Pacific humpback dolphin (Sousa chinensis) habitat in the Northern Beibu Gulf, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:6957-6970. [PMID: 30644049 DOI: 10.1007/s11356-018-3976-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
The northern Beibu Gulf is one of the major habitats for the Indo-Pacific humpback dolphin (Sousa chinensis) in China. In this habitat, the core distribution zone of humpback dolphins was confined to the Sanniang Bay (SNB) and Dafengjiang River Estuary (DRE) areas. In our present research, the sediments of 14 sampling sites across the SNB and DRE waters were collected and further conducted for microbiomic and environmental analysis to explore the ecosystem characteristics of major humpback dolphin habitats in Northern Beibu Gulf. The environmental condition includes ammonia nitrogen (NH4+-N), nitrate nitrogen (NO3--N), dissolved reactive phosphorus (DRP), sulfur content in the form of sulfuric acid (SO42--S), Fe, and heavy metals (including Cu, Zn, Cd, Pb, and As). The composition of the bacterial community was characterized by 16S ribosomal DNA analysis of the V3-V4 regions using the Illumina-based sequencing platform. The environmental characteristic of the nutrient elements and heavy metals indicated that SNB suffered more anthropogenic impact than DRE. The comparably higher concentration of NH4+-N, NO3--N, DRP, Pb, and Cd in the SNB region was detected. The comparably higher nutrients in the SNB may have resulted in higher biomass and lower dissolved oxygen (DO) profile, which was further proved by Landsat thermal image data. The microbiome analysis showed that the DRE region was oligotrophic and SNB reflected an anaerobic environment in the sediments. Environmental factors rather than the spatial distance determined the similarity of bacterial community among different sites. Ecological associations between environmental, oceanographic, and bacterial characteristics were illustrated, which exhibited strong mutual associations. Our findings presented a feasibility that integrates empirical and remote sensing data to distinguish ecological features and evaluate ecosystem healthiness for the humpback dolphin habitats.
Collapse
Affiliation(s)
- Bin Gong
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, 535000, China
- The Key Laboratory of Coastal Science and Engineering, Qinzhou, 535000, Guangxi, China
| | - Hu Huang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, 535000, China
| | - Chongwei Peng
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, 535000, China
| | - Jingzhen Wang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, 535000, China
| | - Jixian Ma
- Marine Environment Monitoring Center, Qinzhou Oceanic Administration, Qinzhou, 535000, China
| | - Xiangxu Liu
- Marine Environment Monitoring Center, Qinzhou Oceanic Administration, Qinzhou, 535000, China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
| | - Shiang-Lin Huang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, 535000, China.
- Guanxi Beibu Gulf Marine Research Center, Guanxi Academy of Sciences, Nanning, 530007, Guanxi, China.
- College of Science, Shantou University, Shantou, 515000, China.
| | - Haiping Wu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, 535000, China.
| |
Collapse
|
39
|
Quantifying population-specific growth in benthic bacterial communities under low oxygen using H 218O. ISME JOURNAL 2019; 13:1546-1559. [PMID: 30783213 PMCID: PMC6776007 DOI: 10.1038/s41396-019-0373-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 01/09/2023]
Abstract
The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.
Collapse
|
40
|
Candidatus Krumholzibacterium zodletonense gen. nov., sp nov, the first representative of the candidate phylum Krumholzibacteriota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics. Syst Appl Microbiol 2018; 42:85-93. [PMID: 30477901 DOI: 10.1016/j.syapm.2018.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 11/23/2022]
Abstract
The accumulation of genomes of uncultured organisms has highlighted the need for devising a taxonomic and nomenclature scheme to validate names and prevent redundancies. We here report on the recovery and analysis of four phylogenetically related genomes recovered from an anoxic sulfide and sulfur-rich spring (Zodletone spring) in southwestern Oklahoma. Phylogenetic analysis based on 120 single copy markers attested to their position as a novel distinct bacterial phylum. Genomic analysis suggests Gram-negative flagellated organisms that possess type IV pili. The organisms are predicted to be rod-shaped, slow-growers, with an anoxic, heterotrophic, and fermentative lifestyle. Predicted substrate utilization pattern includes multiple amino acids, dipeptides, tripeptides, and oligpopeptides; as well as few sugars. Predicted auxotrophies include proline, vitamin B6, lipoic acid, biotin, and vitamin B12. Assessment of the putative global distribution pattern of this novel lineage suggests its preference to anoxic marine, terrestrial, hydrocarbon-impacted, and freshwater habitats. We propose the candidatus name Krumholzibacterium zodletonense gen. nov, sp. nov. for Zgenome0171T, with the genome serving as the type material for the novel family Krumholzibacteriaceae fam. nov., order Krumholzibacteriales ord. nov., class Krumholzibacteria class nov., and phylum Krumholzibacteriota phyl. nov. The type material genome assembly is deposited in GenBank under accession number QTKG01000000.
Collapse
|
41
|
Pang H, Zhou Z, Niu T, Jiang LM, Chen G, Xu B, Jiang L, Qiu Z. Sludge reduction and microbial structures of aerobic, micro-aerobic and anaerobic side-stream reactor coupled membrane bioreactors. BIORESOURCE TECHNOLOGY 2018; 268:36-44. [PMID: 30071411 DOI: 10.1016/j.biortech.2018.07.097] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
An anoxic/oxic membrane bioreactor (MBR) and three side-stream reactor (SSR) coupled membrane bioreactors were operated in parallel to investigate effects of dissolved oxygen (DO) level in SSR on sludge reduction and microbial community structure of SSR-MBRs. The four MBRs were equally efficient in COD and ammonium nitrogen removal. The anaerobic and micro-aerobic SSR favored nitrogen removal through denitrification, simultaneous nitrification and denitrification and autochthonous substrate release as carbon source. The micro-aerobic SSR achieved greatly higher sludge reduction efficiency (61.1%) than anaerobic (37.3%) and aerobic SSR (7.9%). Micro-aerobic SSR obtained the highest endogenous decay constant (0.035 d-1) compared to anaerobic (0.023 d-1) and aerobic SSR (0.015 d-1). High-throughput sequencing results revealed that anaerobic SSR enriched hydrolytic and fermentative bacteria, aerobic environment favored the growth of slow-growing bacteria, and micro-aerobic SSR stimulated biological activities of both anaerobic and aerobic bacteria.
Collapse
Affiliation(s)
- Hongjian Pang
- College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Zhen Zhou
- College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Tianhao Niu
- College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Lu-Man Jiang
- College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Guang Chen
- Shanghai Chentou Wastewater Treatment Co., Ltd, Shanghai 201203, China
| | - Biao Xu
- College of Environmental and Chemical Engineering, Shanghai University of Electric Power, Shanghai 200090, China
| | - Lingyan Jiang
- Shanghai Chentou Wastewater Treatment Co., Ltd, Shanghai 201203, China
| | - Zhan Qiu
- Shanghai Chentou Wastewater Treatment Co., Ltd, Shanghai 201203, China
| |
Collapse
|
42
|
Sarhan MS, Patz S, Hamza MA, Youssef HH, Mourad EF, Fayez M, Murphy B, Ruppel S, Hegazi NA. G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla. Microbes Environ 2018; 33:317-325. [PMID: 30210099 PMCID: PMC6167109 DOI: 10.1264/jsme2.me18023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022] Open
Abstract
The rapid development of high-throughput techniques and expansion of bacterial databases have accelerated efforts to bring plant microbiomes into cultivation. We introduced plant-only-based culture media as a successful candidate to mimic the nutritional matrices of plant roots. We herein employed a G3 PhyloChip microarray to meticulously characterize the culture-dependent and -independent bacterial communities of the maize root compartments, the endo- and ecto-rhizospheres. An emphasis was placed on the preference of the growth of unculturable candidate divisions/phyla on plant-only-based culture media over standard culture media (nutrient agar). A total of 1,818 different operational taxonomic units (OTUs) were resolved representing 67 bacterial phyla. Plant-only-based culture media displayed particular affinity towards recovering endophytic over ectophytic rhizobacteria. This was shown by the slightly higher recovery of CFUs for endophytes on plant-only-based culture media (26%) than on standard culture media (10%) as well as the higher taxa richness and numbers of exclusive families of unculturable divisions/phyla. Out of 30 bacterial phyla (comprising >95% of the whole population), 13 were of a significantly higher incidence on plant-only-based culture media, 6 phyla of which were not-yet-cultured (Atribacteria, OP9; Dependentiae, TM6; Latescibacteria, WS3; Marinimicrobia, SAR406; Omnitrophica, OP3; BRC1). Furthermore, plant-only-based culture media significantly enriched less abundant and/or hard-to-culture bacterial phyla (Acidobacteria, Gemmatimonadetes, and Tenericutes). These results present conclusive evidence of the ability of plant-only-based culture media to bring the plant-fed in situ microbiome into the status of plant-fed in vitro cultures, and to widen the scope of cultivation of heretofore-unculturable bacterial divisions/phyla.
Collapse
Affiliation(s)
- Mohamed S. Sarhan
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Sascha Patz
- Algorithms in Bioinformatics, Center for Bioinformatics, University of TübingenTübingen, 72076Germany
| | - Mervat A. Hamza
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Hanan H. Youssef
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Elhussein F. Mourad
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Brian Murphy
- Department of Botany, School of Natural Sciences, Trinity College DublinDublin 2Ireland
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V. (IGZ)Großbeeren, 14979Germany
| | - Nabil A. Hegazi
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| |
Collapse
|
43
|
El-Chakhtoura J, Saikaly PE, van Loosdrecht MCM, Vrouwenvelder JS. Impact of Distribution and Network Flushing on the Drinking Water Microbiome. Front Microbiol 2018; 9:2205. [PMID: 30283424 PMCID: PMC6157312 DOI: 10.3389/fmicb.2018.02205] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/29/2018] [Indexed: 11/30/2022] Open
Abstract
We sampled the tap water of seven unique, full-scale drinking water distribution systems at different locations as well as the corresponding treatment plant effluents to evaluate the impact of distribution and the potential presence of a core drinking water microbiome. The water was also sampled during network flushing to examine its effect on the microbial ecology. While a core microbiome dominated by Gammaproteobacteria was found using 16S rRNA gene pyrosequencing, an increase in biomass was detected in the networks, especially during flushing. Water age did not significantly impact the microbiology. Irrespective of differences in treatment plants, tap water bacterial communities in the distinct networks converged and highly resembled the flushed water communities. Piping biofilm and sediment communities therefore largely determine the final tap water microbial quality, attenuating the impact of water source and treatment strategy and highlighting the fundamental role of local physicochemical conditions and microbial processes within infrastructure micro-niches.
Collapse
Affiliation(s)
- Joline El-Chakhtoura
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands.,Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Pascal E Saikaly
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Johannes S Vrouwenvelder
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands.,Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| |
Collapse
|
44
|
Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing. Appl Environ Microbiol 2018; 84:AEM.01083-18. [PMID: 29980553 PMCID: PMC6122004 DOI: 10.1128/aem.01083-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 06/28/2018] [Indexed: 11/20/2022] Open
Abstract
Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ “dark” primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover. Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [13C]bicarbonate, DNA-qSIP showed that ammonia-oxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter. Natural 13C-labeled organic matter was then obtained by incubating sediments in the dark for 2.5 months with [13C]bicarbonate, followed by extraction and concentration of high-molecular-weight (HMW) (>50-kDa) organic matter. qSIP showed that the labeled organic matter was turned over within 1 week by 823 microbial populations (operational taxonomic units [OTUs]) affiliated primarily with heterotrophic Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes. However, several OTUs affiliated with the candidate microbial taxa Latescibacteria, Omnitrophica, Aminicentantes, Cloacimonates, AC1, Bathyarchaeota, and Woesearchaeota, groups known only from genomic signatures, also contributed to biomass turnover. Of these 823 labeled OTUs, 52% (primarily affiliated with Proteobacteria) also became labeled in 1-week incubations with [13C]bicarbonate, indicating that they turned over carbon faster than OTUs that were labeled only in incubations with 13C-labeled HMW organic matter. These taxa consisted primarily of uncultivated populations within the Firmicutes, Bacteroidetes, Verrucomicrobia, and Chloroflexi, highlighting their ecological importance. Our study helps define the role of several poorly understood, uncultivated microbial groups in the turnover of benthic carbon derived from “dark” primary production. IMPORTANCE Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ “dark” primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover.
Collapse
|
45
|
Miranda ARL, Antunes JEL, de Araujo FF, Melo VMM, Bezerra WM, Van den Brink PJ, Araujo ASFD. Less abundant bacterial groups are more affected than the most abundant groups in composted tannery sludge-treated soil. Sci Rep 2018; 8:11755. [PMID: 30082922 PMCID: PMC6079073 DOI: 10.1038/s41598-018-30292-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/27/2018] [Indexed: 11/13/2022] Open
Abstract
The application of composted tannery sludge (CTS) has promoted shifts in soil chemical properties and, therefore, can affect the soil bacterial community. This study assessed the effect of the CTS on the soil bacterial community over time. The CTS was applied at five rates (0, 2.5, 5, 10 and 20 t/ha), and the bacterial community was evaluated for 180 days. The principal curve response (PRC) analysis showed that the most abundant phyla were not influenced by the CTS rates over time, while the analysis of the bacterial community showed that some of the less abundant phyla were influenced by the CTS rates. Similarly, the PRC analysis for the bacterial classes showed the significant effect of the CTS rates. The redundancy analyses for the bacterial phyla and classes showed the relationship between the significant chemical properties and the bacterial community of the soil after the CTS amendment over time. Therefore, there was a shift in the bacterial community over time with the application of the composted tannery sludge. Our study has shown that the less abundant bacterial groups were more influenced by the CTS than the most abundant bacterial groups and that these bacterial groups were driven by soil chemical properties, primarily chromium (Cr) and the soil pH.
Collapse
Affiliation(s)
- Ana Roberta Lima Miranda
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil
| | - Jadson Emanuel Lopes Antunes
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil
| | | | | | | | - Paul J Van den Brink
- Wageningen University, Aquatic Ecology and Water Quality Management Group, Wageningen, P.O. Box 47, 6700 AA, The Netherlands
- Wageningen Environmental Research (Alterra), Wageningen, P.O. Box 47, 6700 AA, The Netherlands
| | | |
Collapse
|
46
|
Eissler Y, Gálvez MJ, Dorador C, Hengst M, Molina V. Active microbiome structure and its association with environmental factors and viruses at different aquatic sites of a high-altitude wetland. Microbiologyopen 2018; 8:e00667. [PMID: 30062777 PMCID: PMC6436485 DOI: 10.1002/mbo3.667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/04/2018] [Accepted: 04/21/2018] [Indexed: 01/23/2023] Open
Abstract
Salar de Huasco is a high‐altitude wetland characterized by a highly diverse microbial life adapted to extreme climatic and environmental conditions. Our study aims to determine active microbial community structure changes within different aquatic sites and its relationship with environmental factors and viruses as potential drivers of diversification in different aquatic areas of this ecosystem. In this study, bacteria and archaea composition (16S rRNA subunit pyrolibraries) and picoplankton and viral abundance were determined at ponds, springs and lagoon sites of the wetland during wet and dry seasons (February and July 2012, respectively). In general, mixosaline waters (1,400–51,000 μS/cm) usually found in ponds and lagoon presented higher picoplanktonic abundances compared to freshwater (<800 μS/cm) spring sites, ranging from 1.07 × 105 to 1.83 × 107 cells/ml. Viral abundance and viral to picoplankton ratio (VPR) also presented greater values at ponds compared to spring sites, reaching up to 4.78 × 108 viruses‐like particles and up to 351 for VPR. In general, ponds hold a higher microbial diversity and complexity associated also with the presence of microbial mats compared with water sources or lagoon (Shannon index H′ 2.6–3.9 vs. <2.0). A greater richness of archaea was also detected in ponds characterized by functional groups such as known methanogens and ammonia oxidizers, and uncultured groups. In total, our results indicate that among the different aquatic sites of the wetland, ponds presented a great microbial community diversification associated to a higher top‐down control by viruses which may influence nutrient and greenhouse gases cycling.
Collapse
Affiliation(s)
- Yoanna Eissler
- Facultad de Ciencias, Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Universidad de Valparaíso, Valparaíso, Chile
| | - María-Jesús Gálvez
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha, Valparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Santiago, Chile
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Santiago, Chile.,Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile
| | - Verónica Molina
- Programa de Biodiversidad and Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Observatorio de Ecología Microbiana, Universidad de Playa Ancha, Valparaíso, Chile
| |
Collapse
|
47
|
Kou S, Vincent G, Gonzalez E, Pitre FE, Labrecque M, Brereton NJB. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial. Front Microbiol 2018; 9:366. [PMID: 29545788 PMCID: PMC5838024 DOI: 10.3389/fmicb.2018.00366] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/16/2018] [Indexed: 11/27/2022] Open
Abstract
Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.
Collapse
Affiliation(s)
- Shumeng Kou
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Gilles Vincent
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
| | - Frederic E. Pitre
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
| | | |
Collapse
|
48
|
Espínola F, Dionisi HM, Borglin S, Brislawn CJ, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lozada M. Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. MICROBIAL ECOLOGY 2018; 75:123-139. [PMID: 28702706 DOI: 10.1007/s00248-017-1028-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.
Collapse
Affiliation(s)
- Fernando Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Sharon Borglin
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Walter P Mac Cormack
- Instituto Nanobiotec, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, and ARCEx-Research Centre for Arctic Petroleum Exploration, Department of Geosciences, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
| |
Collapse
|
49
|
Semblante GU, Phan HV, Hai FI, Xu ZQ, Price WE, Nghiem LD. The role of microbial diversity and composition in minimizing sludge production in the oxic-settling-anoxic process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:558-567. [PMID: 28704678 DOI: 10.1016/j.scitotenv.2017.06.253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
The oxic-settling-anoxic (OSA) process, which involves an aerobic tank attached to oxygen- and substrate-deficient external anoxic reactors, minimizes sludge production in biological wastewater treatment. In this study, the microbial community structure of OSA was determined. Principal coordinate analysis showed that among the three operational factors, i.e., (i) redox condition, (ii) external reactor sludge retention time (SRText), and (iii) sludge interchange between aerobic and anoxic reactors, redox condition had the greatest impact on microbial diversity. Generally, reactors with lower oxidation-reduction potential had higher microbial diversity. The main aerobic sequencing batch reactor of OSA (SBROSA) that interchanged sludge with an external anoxic reactor had greater microbial diversity than SBRcontrol which did not have sludge interchange. SBROSA sustained high abundance of the slow-growing nitrifying bacteria (e.g., Nitrospirales and Nitrosomondales) and consequently exhibited reduced sludge yield. Specific groups of bacteria facilitated sludge autolysis in the external reactors. Hydrolyzing (e.g., Bacteroidetes and Chloroflexi) and fermentative (e.g., Firmicutes) bacteria, which can break down cellular matter, proliferated in both the external aerobic/anoxic and anoxic reactors. Sludge autolysis in the anoxic reactor was enhanced with the increase of predatory bacteria (e.g., order Myxobacteriales and genus Bdellovibrio) that can contribute to biomass decay. Furthermore, β- and γ-Proteobacteria were identified as the bacterial phyla that primarily underwent decay in the external reactors.
Collapse
Affiliation(s)
- Galilee U Semblante
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Hop V Phan
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Faisal I Hai
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia.
| | - Zhi-Qiang Xu
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - William E Price
- Strategic Water Infrastructure Laboratory, School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Long D Nghiem
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| |
Collapse
|
50
|
Astudillo-García C, Slaby BM, Waite DW, Bayer K, Hentschel U, Taylor MW. Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges. Environ Microbiol 2017; 20:561-576. [DOI: 10.1111/1462-2920.13965] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/20/2017] [Accepted: 10/19/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Carmen Astudillo-García
- School of Biological Sciences; University of Auckland; Auckland New Zealand
- Institute of Marine Science, University of Auckland; Auckland New Zealand
| | - Beate M. Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences, University of Würzburg; Würzburg Germany
| | - David W. Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences; The University of Queensland; QLD, St Lucia Australia
| | - Kristina Bayer
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- Christian-Albrechts-Universität zu Kiel; Kiel Germany
| | - Michael W. Taylor
- School of Biological Sciences; University of Auckland; Auckland New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland; New Zealand
| |
Collapse
|