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Pradel N, Bartoli M, Koenen M, Bale N, Neumann-Schaal M, Spröer C, Bunk B, Rohde M, Pester M, Spring S. Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov. PLoS One 2024; 19:e0308405. [PMID: 39186748 PMCID: PMC11346949 DOI: 10.1371/journal.pone.0308405] [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: 03/15/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.
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Affiliation(s)
- Nathalie Pradel
- CNRS/INSU, IRD, MIO, UM 110, Aix-Marseille Université, Université du Sud Toulon-Var, Marseille, France
| | - Manon Bartoli
- CNRS/INSU, IRD, MIO, UM 110, Aix-Marseille Université, Université du Sud Toulon-Var, Marseille, France
| | - Michel Koenen
- Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Nicole Bale
- Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department Bioinformatics, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Yan W, Wang D, Wang Y, Wang C, Chen X, Liu L, Wang Y, Li YY, Kamagata Y, Nobu MK, Zhang T. Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities. MICROBIOME 2024; 12:121. [PMID: 38970122 PMCID: PMC11225162 DOI: 10.1186/s40168-024-01830-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry. RESULTS In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role. CONCLUSION Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.
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Affiliation(s)
- Weifu Yan
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu-You Li
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Masaru K Nobu
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao SAR, China.
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Geesink P, ter Horst J, Ettema TJG. More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities. FEMS Microbiol Ecol 2024; 100:fiae029. [PMID: 38444203 PMCID: PMC10950044 DOI: 10.1093/femsec/fiae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members. The production of certain metabolites that can be tied to a specific microbe-microbe interaction might subsequently influence the physicochemical parameters of the habitat, stimulate a change in the trophic network of the community or create new micro-habitats through the formation of biofilms, similar to the production of antimicrobial substances which might negatively affect only one microorganism but cause a ripple effect on the abundance of other community members. Here, we argue that combining established as well as innovative laboratory and computational methods is needed to predict novel interactions and assess their secondary effects. Such efforts will enable future microbiome studies to expand our knowledge on the dynamics of complex microbial communities.
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Affiliation(s)
- Patricia Geesink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jolanda ter Horst
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Ye H, Tu N, Wu Z, He S, Zhao Y, Yue M, Hong M. Identification of bacteria and fungi responsible for litter decomposition in desert steppes via combined DNA stable isotope probing. Front Microbiol 2024; 15:1353629. [PMID: 38525080 PMCID: PMC10957780 DOI: 10.3389/fmicb.2024.1353629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/28/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Soil microorganisms play crucial roles in determining the fate of litter in desert steppes because their activities constitute a major component of the global carbon (C) cycle. Human activities lead to increased ecosystem nitrogen (N) deposition, which has unpredictable impacts on soil microorganism diversity and functions. Nowadays, it is necessary to further study the succession of these microorganisms in the process of litter decomposition in desert steppe, and explore the effect of N deposition on this process. This issue is particularly important to resolve because it contributes to the broader understanding of nutrient cycling processes in desert steppes. Methods In this study, DNA stable isotope probing (DNA-SIP) was used to study changes in soil bacterial and fungal community composition and function during 8 weeks of culture of 13C-labeled litter in desert steppes. Results The results were as follows: (1) Actinomycetota, Pseudomonadota, and Ascomycota are the main microorganisms involved in litter decomposition in desert steppes; (2) N deposition (50 kg ha-1 year-1) significantly increased the relative abundance of some microorganisms involved in the decomposition process; and (3) N deposition likely promotes litter decomposition in desert steppes by increasing the abundances of N cycles bacteria (usually carrying GH family functional genes). Discussion These findings contribute to a deeper understanding of the C assimilation mechanisms associated with litter residue production, emphasizing the importance of extensive C utilization.
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Affiliation(s)
- He Ye
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Nare Tu
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Zhendan Wu
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Shilong He
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Yu Zhao
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Mei Yue
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Mei Hong
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
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Centurion VB, Rossi A, Orellana E, Ghiotto G, Kakuk B, Morlino MS, Basile A, Zampieri G, Treu L, Campanaro S. A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes. ENVIRONMENTAL MICROBIOME 2024; 19:1. [PMID: 38167520 PMCID: PMC10762816 DOI: 10.1186/s40793-023-00545-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production. RESULTS The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs. CONCLUSIONS This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization.
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Affiliation(s)
| | - Alessandro Rossi
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Esteban Orellana
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Gabriele Ghiotto
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, 12 Somogyi B. U. 4., Szeged, 6720, Hungary
| | - Maria Silvia Morlino
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Arianna Basile
- MRC Toxicology Unit, University of Cambridge, Gleeson Building Tennis Court Road, Cambridge, UK
| | - Guido Zampieri
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy.
| | - Laura Treu
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
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Ma J, Yao Z, Zhao L. Comprehensive study of the combined effects of biochar and iron-based conductive materials on alleviating long chain fatty acids inhibition in anaerobic digestion. ENVIRONMENTAL RESEARCH 2023; 239:117446. [PMID: 37858695 DOI: 10.1016/j.envres.2023.117446] [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: 08/19/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]
Abstract
This study investigated the feasibility of alleviating the negative influence of long-chain fatty acids (LCFAs) on anaerobic digestion by biochar, micron zero-valent iron, micron-magnetite (mFe3O4) and their combination. The results demonstrate that co-addition of biochar and 6 g/L mFe3O4 (BC+6 g/L mFe3O4) increased cumulative methane production by 50% as suffered from LCFAs inhibition exerted by 2 g/L glycerol trioleate. The BC+6 g/L mFe3O4 did best in accelerating total organic carbon degradation and volatile fatty acids conversion, through successively enriching Bacteroides, Corynebacterium, and DMER64 to dominant the bacterial community. The proportion of acetotrophic Methanothrix that could alternatively reduce CO2 to methane by accepting electrons via direct interspecies electron transfer (DIET) was 0.09% with BC+6 g/L mFe3O4, nine times more than the proportion in control. Prediction of functional genes revealed the enrichment of the bacterial secretion system, indicating that BC+6 g/L mFe3O4 promoted DIET by stimulating the secretion of extracellular polymeric substances. This study provided novel insights into combining biochar and iron-based conductive materials to enhance AD performance under LCFAs inhibition.
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Affiliation(s)
- Junyi Ma
- Key Laboratory of Low-carbon Green Agriculture in North China of Ministry of Agriculture and Rural Affairs, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zonglu Yao
- Key Laboratory of Low-carbon Green Agriculture in North China of Ministry of Agriculture and Rural Affairs, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lixin Zhao
- Key Laboratory of Low-carbon Green Agriculture in North China of Ministry of Agriculture and Rural Affairs, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Li Y, Zhang S, Chen Z, Ye Z, Lyu R. Multi-omics analysis unravels effects of salt and oil on substance transformation, microbial community, and transcriptional activity in food waste anaerobic digestion. BIORESOURCE TECHNOLOGY 2023; 387:129684. [PMID: 37586433 DOI: 10.1016/j.biortech.2023.129684] [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: 06/17/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
In this study, through quantitative detection of key substances and enzyme activities, an integrated analysis of 16S rRNA sequencing and metatranscriptomics revealed the mechanisms by which salt and oil influence the biotransformation process during anaerobic digestion (AD). The results demonstrated that a salt concentration of 6 g/L promoted lipid metabolism and hydrogenotrophic methanogenesis, while inhibiting the acetoclastic pathway. An oil concentration of 5 g/L facilitated the expression of key enzyme-encoding genes involved in β-oxidation of long-chain fatty acids, transcription, and acetoclastic methanogenesis. It also promoted the enrichment of syntrophic propionate/butyrate oxidation bacteria (Syntrophomonas and DMER64). Salt/oil co-addition enhanced the expression of genes related to glucose metabolism, amino acid metabolism, organic acid synthesis, and quorum sensing. Furthermore, salt/oil co-addition inhibited the secretion of key enzymes related to methanogens by impeding the transcription process. Collectively, these findings provide systematic insights into how salt and oil affect the biochemical metabolic mechanisms of AD.
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Affiliation(s)
- Yanzeng Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shenghua Zhang
- College of Harbour and Coastal Engineering, Jimei University, Xiamen 361021, China.
| | - Zhou Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhilong Ye
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Ruoshui Lyu
- Shanghai Guanghua Qidi College, Shanghai 200433, China
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8
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Vyshenska D, Sampara P, Singh K, Tomatsu A, Kauffman WB, Nuccio EE, Blazewicz SJ, Pett-Ridge J, Louie KB, Varghese N, Kellom M, Clum A, Riley R, Roux S, Eloe-Fadrosh EA, Ziels RM, Malmstrom RR. A standardized quantitative analysis strategy for stable isotope probing metagenomics. mSystems 2023; 8:e0128022. [PMID: 37377419 PMCID: PMC10469821 DOI: 10.1128/msystems.01280-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/19/2023] [Indexed: 06/29/2023] Open
Abstract
Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg, an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, "who is eating what?" and "who is active?" within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.
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Affiliation(s)
- Dariia Vyshenska
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Pranav Sampara
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kanwar Singh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Andy Tomatsu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - W. Berkeley Kauffman
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Katherine B. Louie
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Neha Varghese
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew Kellom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alicia Clum
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert Riley
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Emiley A. Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ryan M. Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rex R. Malmstrom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Kligerman DC, Zanatta AS, Toledo GDA, Nogueira JMDR. Path toward Sustainability in Wastewater Management in Brazil. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6597. [PMID: 37623180 PMCID: PMC10454515 DOI: 10.3390/ijerph20166597] [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: 06/05/2023] [Revised: 08/07/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Developing countries have not carried out the adequate management of wastewater and are a long way off meeting the sustainability goal of universal access to safely managed sanitation services by 2030. This article discusses sustainability in wastewater management and conducts a narrative literature review to analyze four stages on the path toward sustainability: (1) the prevention of or reduction in pollution at the source; (2) wastewater collection and treatment; (3) using wastewater as an alternative source of water; and (4) the recovery of useful by-products. It also provides an overview of wastewater management in Brazil and shows the advantages of using wastewater to produce biofuel in a country in which 48.3% of energy production comes from renewable sources.
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Affiliation(s)
- Débora Cynamon Kligerman
- Departamento de Saneamento e Saúde Ambiental (DSSA) (ENSP), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21041-210, Brazil;
| | - Aline Stelling Zanatta
- Instituto de Ciência e Tecnologia em Biomodelos (ICTB), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, Brazil;
| | - Graziella de Araújo Toledo
- Departamento de Saneamento e Saúde Ambiental (DSSA) (ENSP), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21041-210, Brazil;
| | - Joseli Maria da Rocha Nogueira
- Laboratório de Microbiologia do Departamento de Ciências Biológicas (DCB) (ENSP), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21041-210, Brazil;
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10
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Jin Y, Lu Y. Syntrophic Propionate Oxidation: One of the Rate-Limiting Steps of Organic Matter Decomposition in Anoxic Environments. Appl Environ Microbiol 2023; 89:e0038423. [PMID: 37097179 PMCID: PMC10231205 DOI: 10.1128/aem.00384-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Syntrophic propionate oxidation is one of the rate-limiting steps during anaerobic decomposition of organic matter in anoxic environments. Syntrophic propionate-oxidizing bacteria (SPOB) are members of the "rare biosphere" living at the edge of the thermodynamic limit in most natural habitats. Hitherto, only 10 bacterial species capable of syntrophic propionate oxidization have been identified. SPOB employ different metabolisms for propionate oxidation (e.g., methylmalonyl-CoA pathway and C6 dismutation pathway) and show diverse life strategies (e.g., obligately and facultatively syntrophic lifestyle). The flavin-based electron bifurcation/confurcation (FBEB/C) systems have been proposed to help solve the thermodynamic dilemma during the formation of the low-potential products H2 and formate. Molecular ecological approaches, such as DNA stable isotope probing (DNA-SIP) and metagenomics, have been used to detect SPOB in natural environments. Furthermore, the biogeographical pattern of SPOB has been recently described in paddy soils. A comprehensive understanding of SPOB is essential for better predicting and managing organic matter decomposition and carbon cycling in anoxic environments. In this review, we described the critical role of syntrophic propionate oxidation in anaerobic decomposition of organic matter, phylogenetic and metabolic diversity, life strategies and ecophysiology, composition of syntrophic partners, and pattern of biogeographic distribution of SPOB in natural environments. We ended up with a few perspectives for future research.
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Affiliation(s)
- Yidan Jin
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
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11
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Xu Y, Teng Y, Wang X, Ren W, Zhao L, Luo Y, Christie P, Greening C. Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil. ENVIRONMENT INTERNATIONAL 2023; 176:107962. [PMID: 37196568 DOI: 10.1016/j.envint.2023.107962] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of 13C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.
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Affiliation(s)
- Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ling Zhao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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Ye M, Li YY. Methanogenic treatment of dairy wastewater: A review of current obstacles and new technological perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161447. [PMID: 36621500 DOI: 10.1016/j.scitotenv.2023.161447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/28/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Methanogenic treatment can effectively manage wastewater in the dairy industry. However, its treatment efficiency and stability are problematic due to the feature of wastewater. This review comprehensively summarizes the dairy wastewater characteristics and reveals the mechanisms and impacts of three critical issues in anaerobic treatment, including ammonia and long-chain fatty acid (LCFA) inhibition and trace metal (TM) deficiency. It evaluates current remedial strategies and the implementation of anaerobic membrane bioreactor (AnMBR) technology. It assesses the use of nitrogen-removed effluent return to dilute the influent for solving protein-rich dairy wastewater treatment. It explores the methodology of TM addition to dairy wastewater in accordance with microbial TM content and proliferation. It analyzes the multiple benefits of applying high-solid AnMBR to lipid-rich influent to mitigate LCFA inhibition. Finally, it proposes a promising low-carbon treatment system with enhanced bioenergy recovery, nitrogen removal, and simultaneous phosphorus recovery that could promote carbon neutrality for dairy industry wastewater treatment.
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Affiliation(s)
- Min Ye
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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Duan JL, Han Y, Feng LJ, Ma JY, Sun XD, Liu XY, Geng FS, Jiang JL, Liu MY, Sun YC, Peu P, Ni BJ, Yuan XZ. Single bubble probe atomic force microscope and impinging-jet technique unravel the interfacial interactions controlled by long chain fatty acid in anaerobic digestion. WATER RESEARCH 2023; 231:119657. [PMID: 36709568 DOI: 10.1016/j.watres.2023.119657] [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: 11/03/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Anaerobic digestion of lipid-rich wastewater generally suffers from foaming induced by long chain fatty acid (LCFA). However, a systematic understanding of LCFA inhibition, especially the physical inhibition on interfacial interaction still remains unclear. Here, we combined bubble probe atomic force microscope and impinging-jet technique to unravel the interfacial interactions controlled by long chain fatty acids in anaerobic digestion. We showed that LCFA had a significant inhibition on methane production in anaerobic reactors for the inhibition of the conversion of VFAs to methane. By measuring the LCFA influence on methanogenic archaea Methanosarcina acetivorans C2A, the results demonstrated that methanogenesis was limited for substrates utilization but not metabolic pathways. The impinging-jet technique results indicated that LCFA enhanced bubble separation from anaerobic granules and reduced the bubble-bubble coalescence probability. In addition, the bubble probe atomic force microscope (AFM) revealed that LCFA enhanced the adhesion force between bubbles by enhancing electrical double layer (EDL) repulsion and decreasing hydrophobic interactions. Overall, these results complement framework of LCFA inhibition in anerobic digestion and provide a nanomechanical insight into the fundamental interfacial interactions related to bubbles in anaerobic reactors.
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Affiliation(s)
- Jian-Lu Duan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Yi Han
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Li-Juan Feng
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Jing-Ya Ma
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiao-Dong Sun
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiao-Yu Liu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Fan-Shu Geng
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Jia-Li Jiang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Mei-Yan Liu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Yu-Chen Sun
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China
| | - Pascal Peu
- Department of Ecotechnologies, French National Institute for Agriculture, Food, and Environment (INRAE), Rennes 35044, France; Sino-French Research Institute for Ecology and Environment (ISFREE), Shandong University, Qingdao, Shandong 266237, PR China
| | - Bing-Jie Ni
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, Australia.
| | - Xian-Zheng Yuan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, PR China; Sino-French Research Institute for Ecology and Environment (ISFREE), Shandong University, Qingdao, Shandong 266237, PR China.
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Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants. THE ISME JOURNAL 2023; 17:671-681. [PMID: 36774445 PMCID: PMC9919749 DOI: 10.1038/s41396-023-01378-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/13/2023]
Abstract
The operation of modern wastewater treatment plants (WWTPs) is driven by activated sludge microbiota, a complex assemblage of trophically interacting microorganisms. Microbial predation is crucial to fundamental understanding of how biological interactions drive microbiome structuring and functioning of WWTPs. However, predatory bacteria have received little attention regarding their diversity, activity, and ecological function in activated sludge, limiting the exploitation of food web interactions for wastewater microbiome engineering. Here, by using rRNA-stable isotope probing of activated sludge microbiota with 13C-labeled prey bacteria, we uncovered diverse as-yet-uncultivated putative predatory bacteria that actively incorporated 13C-biomass. Myxobacteria, especially Haliangium and the mle1-27 clade, were found as the dominant active predators, refreshing conventional views based on a few predatory isolates of Bdellovibrionota from WWTPs. The identified predatory bacteria showed more selective predation on prey compared with the protists dominated by ciliates, providing in situ evidence for inter-domain predation behavior divergence in activated sludge. Putative predatory bacteria were tracked over a two-year microbiome monitoring effort at a local WWTP, revealing the predominance of Myxococcota (6.5 ± 1.3%) over Bdellovibrionota (1.0 ± 0.2%) lineages. Phylogenetic analysis unveiled highly diverse myxobacteria inhabiting activated sludge and suggested a habitat filtering effect in global WWTPs. Further mining of a global activated sludge microbiome dataset revealed the prevalence of Myxococcota (5.4 ± 0.1%) species and potential impacts of myxobacterial predation on process performance. Collectively, our findings provided unique insights into the predating activity, diversity, and prevalence of Myxococcota species in activated sludge, highlighting their links with wastewater treatment processes via trophic regulation of enteric and functional bacteria.
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Chen Z, Meng F, Zhou C, Wu X, Jin C. Optimum relative frequency and fluctuating substrate selection in reinforcing anammox-mediated anabolic adaptation. WATER RESEARCH 2023; 228:119377. [PMID: 36427463 DOI: 10.1016/j.watres.2022.119377] [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: 06/07/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Adaptation to substrate fluctuations is a life actuality of microbes in global municipal wastewater treatment plants (WWTPs). Yet there remains a lack of definite information on how influent changes with different alternation frequencies shape the stability of anammox consortia and the metabolic regulations they feedback. According to human rhythmic activity, day-fluctuant fed (every 6 h, alternating between 50 and 100 mg NH4+-N/L) substantially diminished the robustness of nitrogen removal efficiency (NRE; 84.1 ± 7.0%, left-skewed distribution [R2 = 0.87]) and shock-resistance ability (>30% effluent variability). Unexpectedly, the anammox ecosystem under week-fluctuant mode (every 6 d) displayed adapted growth (NRE 86.6 ± 3.1%, normal distribution [R2 = 0.97]), higher extracellular polymeric substances (EPS) yields, and superior tolerance (juggling the shortest recovery time and highest NRE, tightest protein secondary structure facing long-term load shocks) than steady-state (75 mg NH4+-N/L). 16S sequencing showed that the influent disturbance led to increased levels of bacterial diversity, however, a similar microbiota composition between week-fluctuant and steady systems was detected. Notably, K strategist Candidatus Kuenenia was more sensitive to substrate fluctuations, with the lower relative abundance at day-fluctuant (23.4 ± 5.1%) and week-fluctuant (39.5 ± 4.3%) than at steady-state community (47.5 ± 4.2%). Conversely, Candidatus Jettenia had higher relative abundance at day-fluctuant (i.e., 1.3 ± 0.1%) compared to that at week-fluctuant (0.2 ± 0.04%) and steady-state (0.05 ± 0.03%). Importantly, untargeted metabolomics revealed that week-fluctuant grown anammox microbiota increased protein synthesis and transporter expression while decreasing expression of catabolic pathways (citric acid cycle and bypass) as a strategy for efficient substrate uptake and utilization, which clearly different to day-fluctuant and steady-state survival ways. Overall, we predictively reported an "anabolic adaptation growth state" for the anammox consortia and put forward the associated reinforcement control strategy.
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Affiliation(s)
- Zijian Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China
| | - Chuyuan Zhou
- School of Environmental Science and Engineering, Sun Yat-sen University, No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China
| | - Xiaowei Wu
- School of Environmental Science and Engineering, Sun Yat-sen University, No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China
| | - Chao Jin
- School of Environmental Science and Engineering, Sun Yat-sen University, No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), No. 132, Outer Ring East Road, Xiaoguwei Street, Higher Education Mega Center, Guangzhou 510275, China.
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16
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Eliasson KA, Singh A, Isaksson S, Schnürer A. Co-substrate composition is critical for enrichment of functional key species and for process efficiency during biogas production from cattle manure. Microb Biotechnol 2022; 16:350-371. [PMID: 36507711 PMCID: PMC9871532 DOI: 10.1111/1751-7915.14194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/14/2022] Open
Abstract
Cattle manure has a low energy content and high fibre and water content, limiting its value for biogas production. Co-digestion with a more energy-dense material can improve the output, but the co-substrate composition that gives the best results in terms of degree of degradation, gas production and digestate quality has not yet been identified. This study examined the effects of carbohydrate, protein and fat as co-substrates for biogas production from cattle manure. Laboratory-scale semi-continuous mesophilic reactors were operated with manure in mono-digestion or in co-digestion with egg albumin, rapeseed oil, potato starch or a mixture of these, and chemical and microbiological parameters were analysed. The results showed increased gas yield for all co-digestion reactors, but only the reactor supplemented with rapeseed oil showed synergistic effects on methane yield. The reactor receiving potato starch indicated improved fibre degradation, suggesting a priming effect by the easily accessible carbon. Both these reactors showed increased species richness and enrichment of key microbial species, such as fat-degrading Syntrophomonadaceae and families known to include cellulolytic bacteria. The addition of albumin promoted enrichment of known ammonia-tolerant syntrophic acetate- and potential propionate-degrading bacteria, but still caused slight process inhibition and less efficient overall degradation of organic matter in general, and of cellulose in particular.
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Affiliation(s)
| | - Abhijeet Singh
- Department of Molecular Sciences, BioCenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Simon Isaksson
- Department of Molecular Sciences, BioCenterSwedish University of Agricultural SciencesUppsalaSweden
| | - Anna Schnürer
- Department of Molecular Sciences, BioCenterSwedish University of Agricultural SciencesUppsalaSweden
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17
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Zhang N, Wu C, Zhang J, Han S, Peng Y, Song X. Impacts of lipids on the performance of anaerobic membrane bioreactors for food wastewater treatment. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.121104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Rossi A, Morlino MS, Gaspari M, Basile A, Kougias P, Treu L, Campanaro S. Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction. MICROBIOME 2022; 10:125. [PMID: 35965344 PMCID: PMC9377139 DOI: 10.1186/s40168-022-01316-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle. RESULTS The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale. CONCLUSIONS Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters. Video Abstract.
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Affiliation(s)
- Alessandro Rossi
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Gaspari
- Department of Hydraulics, Soil Science and Agricultural Engineering, Faculty of Agriculture, Aristotle University of Thessaloniki, GR-54124, Thessaloniki, Greece
| | - Arianna Basile
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Panagiotis Kougias
- Soil and Water Resources Institute, Hellenic Agricultural Organisation Demeter, Thermi, 57001, Thessaloniki, Greece
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
- CRIBI biotechnology center, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
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Abstract
Noncoding RNAs with secondary structures play important roles in CRISPR-Cas systems. Many of these structures likely remain undiscovered. We used a large-scale comparative genomics approach to predict 156 novel candidate structured RNAs from 36,111 CRISPR-Cas systems. A number of these were found to overlap with coding genes, including palindromic candidates that overlapped with a variety of Cas genes in type I and III systems. Among these 156 candidates, we identified 46 new models of CRISPR direct repeats and 1 tracrRNA. This tracrRNA model occasionally overlapped with predicted cas9 coding regions, emphasizing the importance of expanding our search windows for novel structure RNAs in coding regions. We also demonstrated that the antirepeat sequence in this tracrRNA model can be used to accurately assign thousands of predicted CRISPR arrays to type II-C systems. This study highlights the importance of unbiased identification of candidate structured RNAs across CRISPR-Cas systems.
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Affiliation(s)
- Brayon J. Fremin
- Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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20
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Holohan BC, Duarte MS, Szabo-Corbacho MA, Cavaleiro AJ, Salvador AF, Pereira MA, Ziels RM, Frijters CTMJ, Pacheco-Ruiz S, Carballa M, Sousa DZ, Stams AJM, O'Flaherty V, van Lier JB, Alves MM. Principles, Advances, and Perspectives of Anaerobic Digestion of Lipids. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4749-4775. [PMID: 35357187 DOI: 10.1021/acs.est.1c08722] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Several problems associated with the presence of lipids in wastewater treatment plants are usually overcome by removing them ahead of the biological treatment. However, because of their high energy content, waste lipids are interesting yet challenging pollutants in anaerobic wastewater treatment and codigestion processes. The maximal amount of waste lipids that can be sustainably accommodated, and effectively converted to methane in anaerobic reactors, is limited by several problems including adsorption, sludge flotation, washout, and inhibition. These difficulties can be circumvented by appropriate feeding, mixing, and solids separation strategies, provided by suitable reactor technology and operation. In recent years, membrane bioreactors and flotation-based bioreactors have been developed to treat lipid-rich wastewater. In parallel, the increasing knowledge on the diversity of complex microbial communities in anaerobic sludge, and on interspecies microbial interactions, contributed to extend the knowledge and to understand more precisely the limits and constraints influencing the anaerobic biodegradation of lipids in anaerobic reactors. This critical review discusses the most important principles underpinning the degradation process and recent key discoveries and outlines the current knowledge coupling fundamental and applied aspects. A critical assessment of knowledge gaps in the field is also presented by integrating sectorial perspectives of academic researchers and of prominent developers of anaerobic technology.
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Affiliation(s)
- B Conall Holohan
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway H91 TK33, Ireland
- NVP Energy Ltd., IDA Technology and Business Park, Mervue, Galway H91 TK33, Ireland
| | - M Salomé Duarte
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - M Alejandra Szabo-Corbacho
- Department of Environmental Engineering and Water Technology, IHE Delft Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
| | - Ana J Cavaleiro
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - Andreia F Salvador
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - M Alcina Pereira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
| | - Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, 6250 Applied Science Lane, Vancouver, BC V6T 1Z 4, Canada
| | | | - Santiago Pacheco-Ruiz
- Biothane, Veolia Water Technologies, Tanthofdreef 21, 2623 EW Delft, The Netherlands
| | - Marta Carballa
- CRETUS, Department of Chemical Engineering, Universidad de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway H91 TK33, Ireland
| | - Jules B van Lier
- Department of Environmental Engineering and Water Technology, IHE Delft Institute for Water Education, Westvest 7, 2611 AX Delft, The Netherlands
- Section Sanitary Engineering, CEG Faculty, Delft University of Technology, 2628 CN, Delft, The Netherlands
| | - M Madalena Alves
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, Guimarães, Portugal
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Usman M, Zhao S, Jeon BH, Salama ES, Li X. Microbial β-oxidation of synthetic long-chain fatty acids to improve lipid biomethanation. WATER RESEARCH 2022; 213:118164. [PMID: 35176594 DOI: 10.1016/j.watres.2022.118164] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
β-oxidation is a well-known pathway for fatty acid (FA) degradation. However, the wide range of feedstocks, their intermediates, and complex microbial networks involved in anaerobic digestion (AD) make β-oxidation unclear during lipid digestion having a variety of long-chain fatty acids (LCFAs). Here, we demonstrated the detailed metabolic pathway of major bacteria and enzymes responsible for the β-oxidation of individual saturated FAs (C16:0 and C18:0) and unsaturated FAs (C18:1 and C18:2). C16:0 showed no negative impact on AD. The relative enzyme abundance and production of shorter-chain FAs (
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Affiliation(s)
- Muhammad Usman
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China; Department of Occupational and Environmental Health, School of Public Health, Lanzhou University Lanzhou 730000, Gansu, China
| | - Shuai Zhao
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Korea
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University Lanzhou 730000, Gansu, China.
| | - Xiangkai Li
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China.
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22
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Sun H, Huang K, Zhang X, Ren H, Ye L. Stable isotope probing reveals specific assimilating bacteria of refractory organic compounds in activated sludge. WATER RESEARCH 2022; 212:118105. [PMID: 35074670 DOI: 10.1016/j.watres.2022.118105] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/16/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Activated sludge in wastewater treatment bioreactors contains diverse bacteria, while little is known about the community structure of bacteria responsible for degradation of refractory organic compounds (ROCs). In this study, 10 ROCs frequently detected in sewage were investigated, and the potential bacteria degrading these ROCs were analyzed by DNA stable isotope probing and high-throughput sequencing. The results showed that the bacterial communities responsible for degradation of different ROCs were largely different. A total of 84 bacterial genera were found to be involved in degrading at least one of the 10 ROCs, however, only six genera (Acinetobacter, Bacteroides, Bosea, Brevundimonas, Lactobacillus and Pseudomonas) were common to all 10 ROCs. This suggests that different ROCs may have specific assimilating bacteria in the activated sludge. Our results also showed that these ROC-degrading bacteria are difficult to isolate by conventional methods and that most of them have relatively low relative abundance in municipal wastewater treatment bioreactors. Development of new technologies to increase the abundance and activity of these bacteria may significantly improve the removal efficiency of ROCs from wastewater.
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Affiliation(s)
- Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China.
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23
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Xia F, Jiang QY, Zhu T, Zou B, Liu H, Quan ZX. Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148470. [PMID: 34166901 DOI: 10.1016/j.scitotenv.2021.148470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 μmol/g d.w.s (μmol per gram dry weight soil) NH4+ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.
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Affiliation(s)
- Fei Xia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiu-Yue Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Huan Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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24
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McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
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Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
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25
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Duan H, He P, Shao L, Lü F. Functional genome-centric view of the CO-driven anaerobic microbiome. THE ISME JOURNAL 2021; 15:2906-2919. [PMID: 33911204 PMCID: PMC8443622 DOI: 10.1038/s41396-021-00983-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 02/02/2023]
Abstract
CO is a promising substrate for producing biochemicals and biofuels through mixed microbial cultures, where carboxydotrophs play a crucial role. The previous investigations of mixed microbial cultures focused primarily on overall community structures, but under-characterized taxa and intricate microbial interactions have not yet been precisely explicated. Here, we undertook DNA-SIP based metagenomics to profile the anaerobic CO-driven microbiomes under 95 and 35% CO atmospheres. The time-series analysis of the isotope-labeled amplicon sequencing revealed the essential roles of Firmicutes and Proteobacteria under high and low CO pressure, respectively, and Methanobacterium was the predominant archaeal genus. The functional enrichment analysis based on the isotope-labeled metagenomes suggested that the microbial cultures under high CO pressure had greater potential in expressing carboxylate metabolism and citrate cycle pathway. The genome-centric metagenomics reconstructed 24 discovered and 24 under-characterized metagenome-assembled genomes (MAGs), covering more than 94% of the metagenomic reads. The metabolic reconstruction of the MAGs described their potential functions in the CO-driven microbiomes. Some under-characterized taxa might be versatile in multiple processes; for example, under-characterized Rhodoplanes sp. and Desulfitobacterium_A sp. could encode the complete enzymes in CO oxidation and carboxylate production, improving functional redundancy. Finally, we proposed the putative microbial interactions in the conversion of CO to carboxylates and methane.
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Affiliation(s)
- Haowen Duan
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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26
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Yadav A, Borrelli JC, Elshahed MS, Youssef NH. Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats. Appl Environ Microbiol 2021; 87:e0094721. [PMID: 34160232 PMCID: PMC8357285 DOI: 10.1128/aem.00947-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/14/2021] [Indexed: 12/19/2022] Open
Abstract
Approaches for recovering and analyzing genomes belonging to novel, hitherto-unexplored bacterial lineages have provided invaluable insights into the metabolic capabilities and ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent and ecologically successful lineages on Earth, yet currently, multiple lineages within this phylum remain unexplored. Here, we utilize genomes recovered from Zodletone Spring, an anaerobic sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil and nonsoil habitats, to examine the metabolic capabilities and ecological role of members of family UBA6911 (group 18) Acidobacteria. The analyzed genomes clustered into five distinct genera, with genera Gp18_AA60 and QHZH01 recovered from soils, genus Ga0209509 from anaerobic digestors, and genera Ga0212092 and UBA6911 from freshwater habitats. All genomes analyzed suggested that members of Acidobacteria group 18 are metabolically versatile heterotrophs capable of utilizing a wide range of proteins, amino acids, and sugars as carbon sources, possess respiratory and fermentative capacities, and display few auxotrophies. Soil-dwelling genera were characterized by larger genome sizes, higher numbers of CRISPR loci, an expanded carbohydrate active enzyme (CAZyme) machinery enabling debranching of specific sugars from polymers, possession of a C1 (methanol and methylamine) degradation machinery, and a sole dependence on aerobic respiration. In contrast, nonsoil genomes encoded a more versatile respiratory capacity for oxygen, nitrite, sulfate, and trimethylamine N-oxide (TMAO) respiration, as well as the potential for utilizing the Wood-Ljungdahl (WL) pathway as an electron sink during heterotrophic growth. Our results not only expand our knowledge of the metabolism of a yet-uncultured bacterial lineage but also provide interesting clues on how terrestrialization and niche adaptation drive metabolic specialization within the Acidobacteria. IMPORTANCE Members of the Acidobacteria are important players in global biogeochemical cycles, especially in soils. A wide range of acidobacterial lineages remain currently unexplored. We present a detailed genomic characterization of genomes belonging to family UBA6911 (also known as group 18) within the phylum Acidobacteria. The genomes belong to different genera and were obtained from soil (genera Gp18_AA60 and QHZH01), freshwater habitats (genera Ga0212092 and UBA6911), and an anaerobic digestor (genus Ga0209509). While all members of the family shared common metabolic features, e.g., heterotrophic respiratory abilities, broad substrate utilization capacities, and few auxotrophies, distinct differences between soil and nonsoil genera were observed. Soil genera were characterized by expanded genomes, higher numbers of CRISPR loci, a larger carbohydrate active enzyme (CAZyme) repertoire enabling monomer extractions from polymer side chains, and methylotrophic (methanol and methylamine) degradation capacities. In contrast, nonsoil genera encoded more versatile respiratory capacities for utilizing nitrite, sulfate, TMAO, and the WL pathway, in addition to oxygen as electron acceptors. Our results not only broaden our understanding of the metabolic capacities within the Acidobacteria but also provide interesting clues on how terrestrialization shaped Acidobacteria evolution and niche adaptation.
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Affiliation(s)
- Archana Yadav
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Jenna C. Borrelli
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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27
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Leggieri PA, Liu Y, Hayes M, Connors B, Seppälä S, O'Malley MA, Venturelli OS. Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annu Rev Biomed Eng 2021; 23:169-201. [PMID: 33781078 PMCID: PMC8277735 DOI: 10.1146/annurev-bioeng-082120-022836] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review, we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.
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Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Yiyi Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Madeline Hayes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Bryce Connors
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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28
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Karki R, Chuenchart W, Surendra KC, Shrestha S, Raskin L, Sung S, Hashimoto A, Kumar Khanal S. Anaerobic co-digestion: Current status and perspectives. BIORESOURCE TECHNOLOGY 2021; 330:125001. [PMID: 33773269 DOI: 10.1016/j.biortech.2021.125001] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 05/18/2023]
Abstract
Anaerobic digestion is a long-established technology for the valorization of diverse organic wastes with concomitant generation of valuable resources. However, mono-digestion (i.e., anaerobic digestion using one feedstock) suffers from challenges associated with feedstock characteristics. Co-digestion using multiple feedstocks provides the potential to overcome these limitations. Significant research and development efforts have highlighted several inherent merits of co-digestion, including enhanced digestibility due to synergistic effects of co-substrates, better process stability, and higher nutrient value of the produced co-digestate. However, studies focused on the underlying effects of diverse co-feedstocks on digester performance and stability have not been synthesized so far. This review fills this gap by highlighting the limitations of mono-digestion and critically examining the benefits of co-digestion. Furthermore, this review discusses synergistic effect of co-substrates, characterization of microbial communities, the prediction of biogas production via different kinetic models, and highlights future research directions for the development of a sustainable biorefinery.
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Affiliation(s)
- Renisha Karki
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Wachiranon Chuenchart
- Department of Civil and Environmental Engineering, University of Hawai'i at Mānoa, 2540 Dole Street, Honolulu, HI 96822, USA
| | - K C Surendra
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA; Global Institute for Interdisciplinary Studies, 44600 Kathmandu, Nepal
| | - Shilva Shrestha
- Joint Bioenergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA
| | - Shihwu Sung
- College of Agriculture, Forestry and Natural Resource Management (CAFNRM), University of Hawai'i at Hilo, 200 W. Kawili Street, Hilo, HI 96720, USA
| | - Andrew Hashimoto
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA; Department of Civil and Environmental Engineering, University of Hawai'i at Mānoa, 2540 Dole Street, Honolulu, HI 96822, USA.
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29
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Hashemi S, Hashemi SE, Lien KM, Lamb JJ. Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production. Microorganisms 2021; 9:microorganisms9061162. [PMID: 34071282 PMCID: PMC8226781 DOI: 10.3390/microorganisms9061162] [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: 04/21/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.
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Affiliation(s)
- Seyedbehnam Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Sayed Ebrahim Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Kristian M. Lien
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Jacob J. Lamb
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
- Department of Electronic Systems, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
- Correspondence:
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30
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Candry P, Ganigué R. Chain elongators, friends, and foes. Curr Opin Biotechnol 2021; 67:99-110. [PMID: 33529974 DOI: 10.1016/j.copbio.2021.01.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/02/2021] [Accepted: 01/07/2021] [Indexed: 12/14/2022]
Abstract
Bioproduction of medium chain carboxylic acids has recently emerged as an alternative strategy to valorize low-value organic waste and side-streams. Key to this route is chain elongation, an anaerobic microbial process driven by ethanol, lactic acid, or carbohydrates. Because these technologies use wastes as feedstocks, mixed microbial communities are often considered as biocatalysts. Understanding and steering these microbiomes is key to optimize bioprocess performance. From a meta-analysis of publicly available sequencing data, we (i) explore how the current collection of isolated chain elongators compares to microbiome members, (ii) discuss the main beneficial and antagonistic interactions with community partners, and (iii) identify the key research gaps and needs to help understand chain elongation microbiomes, and design/steer these novel bioproduction processes.
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Affiliation(s)
- Pieter Candry
- Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA 98195-2700, USA
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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31
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Yu J, Pavia MJ, Deem LM, Crow SE, Deenik JL, Penton CR. DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil. Front Microbiol 2020; 11:587972. [PMID: 33329461 PMCID: PMC7717982 DOI: 10.3389/fmicb.2020.587972] [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] [Accepted: 10/08/2020] [Indexed: 12/03/2022] Open
Abstract
The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.
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Affiliation(s)
- Julian Yu
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Lauren M Deem
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Susan E Crow
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Jonathan L Deenik
- Tropical Plant and Soil Sciences, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Christopher Ryan Penton
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
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Insights into the effects of acetate on the community structure of Candidatus Accumulibacter in biological phosphorus removal system using DNA stable-isotope probing (DNA-SIP). Enzyme Microb Technol 2020; 139:109567. [DOI: 10.1016/j.enzmictec.2020.109567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 11/22/2022]
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Hao J, de Los Reyes Iii FL, He X. Fat, oil, and grease (FOG) deposits yield higher methane than FOG in anaerobic co-digestion with waste activated sludge. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 268:110708. [PMID: 32510442 DOI: 10.1016/j.jenvman.2020.110708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
The formation of fat, oil, and grease (FOG) deposits in sewers is a global challenge for the maintenance of sewer collection systems. Tons of FOG deposits (FDs) are removed from sewer systems every year and present an opportunity for increased methane production via anaerobic co-digestion with waste activated sludge (WAS) at water resource recovery facilities with existing anaerobic digesters. We hypothesized that FDs have higher biomethane potential than that of FOG (e.g., FOG collected in grease interceptors), because of the reduction of inhibition of long chain fatty acids due to saponification. In this study, substantially enhanced methane production was found in anaerobic co-digestion of WAS with FDs within the substrate to inoculum (S/I) ratio range of 0.25-1.2, and the maximum ultimate methane production (685.7 ± 24.1 mL/gVSadded, at S/I = 0.5) was 4.0 times higher than in the control (with WAS only) after 42 days of incubation. Although the lag phase period was longer in FD co-digestion (S/I = 0.5) than in FOG co-digestion (S/I = 0.5) under the same organic loading (gVS) and two times the COD loading, the daily methane production rate became higher after Day 15 in FD co-digestion. Significantly higher cumulative methane production (10.2%, p < 0.05) was obtained in FD co-digestion than in FOG co-digestion after 42-days. Microbial community analysis revealed higher levels of Geobacter in FD co-digestion, possibly suggesting a role for direct interspecies electron transfer (DIET) between Methanosaeta and Geobacter. This work provides fundamental insights supporting anaerobic co-digestion of FDs with WAS, demonstrating the advantages of FDs compared to FOG as co-substrate for enhanced biomethane recovery.
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Affiliation(s)
- Jiahou Hao
- College of Environmental Science and Engineering, Guilin University of Technology, Guangxi, 541006, China
| | - Francis L de Los Reyes Iii
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xia He
- College of Environmental Science and Engineering, Guilin University of Technology, Guangxi, 541006, China.
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Advances in monitoring soil microbial community dynamic and function. J Appl Genet 2020; 61:249-263. [PMID: 32062778 DOI: 10.1007/s13353-020-00549-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 01/17/2020] [Accepted: 02/06/2020] [Indexed: 12/22/2022]
Abstract
Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.
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Hatzenpichler R, Krukenberg V, Spietz RL, Jay ZJ. Next-generation physiology approaches to study microbiome function at single cell level. Nat Rev Microbiol 2020; 18:241-256. [PMID: 32055027 DOI: 10.1038/s41579-020-0323-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2020] [Indexed: 12/14/2022]
Abstract
The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.
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Affiliation(s)
- Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Rachel L Spietz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
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Conversion of waste cooking oil into biogas: perspectives and limits. Appl Microbiol Biotechnol 2020; 104:2833-2856. [DOI: 10.1007/s00253-020-10431-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/24/2020] [Accepted: 02/03/2020] [Indexed: 10/25/2022]
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Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics. ISME JOURNAL 2020; 14:906-918. [PMID: 31896784 PMCID: PMC7082340 DOI: 10.1038/s41396-019-0571-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/20/2019] [Accepted: 12/11/2019] [Indexed: 11/25/2022]
Abstract
Short-chain fatty acid (SCFA) degradation is an important process in methanogenic ecosystems, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on isolates or enrichment cultures, but these may not reflect the true diversity and in situ activities of the syntrophs predominating in full-scale systems. Here we obtained 182 medium to high quality metagenome-assembled genomes (MAGs) from the microbiome of two full-scale anaerobic digesters. The transcriptomic response of individual MAG was studied after stimulation with low concentrations of acetate, propionate, or butyrate, separately. The most pronounced response to butyrate was observed for two MAGs of the recently described genus Candidatus Phosphitivorax (phylum Desulfobacterota), expressing a butyrate beta-oxidation pathway. For propionate, the largest response was observed for an MAG of a novel genus in the family Pelotomaculaceae, transcribing a methylmalonyl-CoA pathway. All three species were common in anaerobic digesters at Danish wastewater treatment plants as shown by amplicon analysis, and this is the first time their syntrophic features involved in SCFA oxidation were revealed with transcriptomic evidence. Further, they also possessed unique genomic features undescribed in well-characterized syntrophs, including the metabolic pathways for phosphite oxidation, nitrite and sulfate reduction.
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Abstract
The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.
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Kurade MB, Saha S, Kim JR, Roh HS, Jeon BH. Microbial community acclimatization for enhancement in the methane productivity of anaerobic co-digestion of fats, oil, and grease. BIORESOURCE TECHNOLOGY 2020; 296:122294. [PMID: 31677410 DOI: 10.1016/j.biortech.2019.122294] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
The methane productivity and long chain fatty acids (LCFAs) degradation capability of unacclimatized seed sludge (USS) and acclimatized seed sludge (ASS) at different substrate ratios of fats oil and grease (FOG) and mixed sewage sludge were investigated in this study. Biogas produced in ASS in initial phase of anaerobic digestion had higher methane content (65-76%) than that in USS (26-73%). The degradation of major LCFAs in the ASS was 22-80%, 33-191%, and 7-64% higher for the substrate ratios of 100:10, 100:20, and 100:30, respectively, as compared to the LCFAs' degradation in USS. Microbial acclimatization increased the population of Firmicutes (40%), Bacteroidetes (32%), Synergistetes (10%), and Euryarchaeota (8%) in ASS, which supported the faster rate of LCFAs degradation for its later conversion to methane. The significant abundance of Syntrophomonas and Methanosarcina genera in ASS supported faster generation rate of methane in an obligatory syntrophic relationship.
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Affiliation(s)
- Mayur B Kurade
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Shouvik Saha
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Jung Rae Kim
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan 609-735, Republic of Korea
| | - Hyun-Seog Roh
- Department of Environmental Engineering, Yonsei University, 1 Yonseidae-gil, Wonju, Gangwon 26493, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
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40
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Salama ES, Jeon BH, Kurade MB, Patil SM, Usman M, Li X, Lim H. Enhanced anaerobic co-digestion of fat, oil, and grease by calcium addition: Boost of biomethane production and microbial community shift. BIORESOURCE TECHNOLOGY 2020; 296:122353. [PMID: 31718843 DOI: 10.1016/j.biortech.2019.122353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
This work focused on the application of calcium (0.1-1% w/v) to overcome the inhibition caused by the high loadings (2% v/v) of fat, oil, and grease (FOG) in the context of biomethane production, organic removal, and microbial community shift. Addition of 0.5% calcium showed maximum biomethane production (6-fold increase); biomethane production decreased following the addition of calcium (>0.5%). The highest organic removal rates were 83 and 89% upon the addition of 0.3 and 0.5% calcium, respectively. Addition of calcium facilitated the growth of bacteria of phylum Firmicutes from the Clostridium, Syntrophomonas, and Sedimentibacter genera. The population of members from the genus Methanosaeta increased after the addition of 0.5% calcium, which is one of the factors responsible for high biomethane production. This study demonstrated that addition of calcium is an attractive strategy to avoid the inhibition of the growth of anaerobic microflora due to the presence of high FOG concentrations.
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Affiliation(s)
- El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, Gansu Province, PR China
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, South Korea.
| | - Mayur B Kurade
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, South Korea
| | - Swapnil M Patil
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, South Korea
| | - Muhammad Usman
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, Gansu Province, PR China; MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, PR China
| | - Xiangkai Li
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, PR China
| | - Hankwon Lim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, South Korea
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Genome-Centered Metagenomics Analysis Reveals the Microbial Interactions of a Syntrophic Consortium during Methane Generation in a Decentralized Wastewater Treatment System. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app10010135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The application of anaerobic digestors to decentralized wastewater treatment systems (DWTS) has gained momentum worldwide due to their ease of operation, high efficiency, and ability to recycle wastewater. However, the microbial mechanisms responsible for the high efficiency and ability of DWTS to recycle wastewater are still unclear. In this study, the microbial community structure and function of two different anaerobic bioreactors (a primary sludge digestor, PSD, and anaerobic membrane bioreactor, AnMBR) of a DWTS located in Germany was investigated using 16S rRNA gene amplicon and metagenomic sequencing, respectively. The results showed that the microbial community structure was remarkably different in PSD and AnMBR. Methanobacteriaceae and Syntrophaceae were identified as the families that significantly differed in abundance between these two bioreactors. We also used genome-centered metagenomics to predict the microbial interactions and methane-generating pathway, which yielded 21 near-complete assembled genomes (MAGs) (average completeness of 93.0% and contamination of 2.9%). These MAGs together represented the majority of the microbial community. MAGs affiliated with methanogenic archaea, including Methanobacterium sp., Methanomicrobiales archaea, Methanomassiliicoccales archaea, and Methanosaeta concilii, were recruited, along with other syntrophic bacterial MAGs associated with anaerobic digestion. Key genes encoding enzymes involved in specific carbohydrate-active and methanogenic pathways in MAGs were identified to illustrate the microbial functions and interactions that occur during anaerobic digestion in the wastewater treatment. From the MAG information, it was predicted that bacteria affiliated with Bacteroidetes, Prolixibacteraceae, and Synergistaceae were the key bacteria involved in anaerobic digestion. In the methane production step, Methanobacterium sp. performed hydrogenotrophic methanogenesis, which reduced carbon dioxide to methane with hydrogen as the primary electron donor. Taken together, our findings provide a clear understanding of the methane-generating pathways and highlight the syntrophic interactions that occur during anaerobic digestion in DWTS.
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Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Löffler FE, O'Malley MA, García Martín H, Pfleger BF, Raskin L, Venturelli OS, Weissbrodt DG, Noguera DR, McMahon KD. Common principles and best practices for engineering microbiomes. Nat Rev Microbiol 2019; 17:725-741. [PMID: 31548653 PMCID: PMC8323346 DOI: 10.1038/s41579-019-0255-9] [Citation(s) in RCA: 249] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 12/16/2022]
Abstract
Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue that structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries of the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture and enabling the bioeconomy.
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Affiliation(s)
- Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
| | - William R Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | | | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbra, CA, USA
- DOE Joint Bioenergy Institute, Emeryville, CA, USA
| | - Héctor García Martín
- DOE Joint Bioenergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- DOE Agile BioFoundry, Emeryville, CA, USA
- Basque Center for Applied Mathematics, Bilbao, Spain
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ophelia S Venturelli
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Daniel R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, Madison, WI, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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Wang HZ, Lv XM, Yi Y, Zheng D, Gou M, Nie Y, Hu B, Nobu MK, Narihiro T, Tang YQ. Using DNA-based stable isotope probing to reveal novel propionate- and acetate-oxidizing bacteria in propionate-fed mesophilic anaerobic chemostats. Sci Rep 2019; 9:17396. [PMID: 31758023 PMCID: PMC6874663 DOI: 10.1038/s41598-019-53849-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/06/2019] [Indexed: 02/07/2023] Open
Abstract
Propionate is one of the most important intermediates of anaerobic fermentation. Its oxidation performed by syntrophic propionate-oxidizing bacteria coupled with hydrogenotrophic methanogens is considered to be a rate-limiting step for methane production. However, the current understanding of SPOB is limited due to the difficulty of pure culture isolation. In the present study, two anaerobic chemostats fed with propionate as the sole carbon source were operated at different dilution rates (0.05 d-1 and 0.15 d-1). The propionate- and acetate-oxidizing bacteria in the two methanogenic chemostats were investigated combining DNA-stable isotope probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing. The results of DNA-SIP with 13C-propionate/acetate suggested that, Smithella, Syntrophobacter, Cryptanaerobacter, and unclassified Rhodospirillaceae may be putative propionate-oxidizing bacteria; unclassified Spirochaetaceae, unclassified Synergistaceae, unclassified Elusimicrobia, Mesotoga, and Gracilibacter may contribute to acetate oxidation; unclassified Syntrophaceae and Syntrophomonas may be butyrate oxidizers. By DNA-SIP, unclassified OTUs with 16S rRNA gene abundance higher than 62% of total Bacteria in the PL chemostat and 38% in the PH chemostat were revealed to be related to the degradation of propionate. These results suggest that a variety of uncultured bacteria contribute to propionate degradation during anaerobic digestion. The functions and metabolic characteristics of these bacteria require further investigation.
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Affiliation(s)
- Hui-Zhong Wang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan, 610065, China
| | - Xiao-Meng Lv
- Institute of New Energy and Low-Carbon Technology, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan, 610065, China
| | - Yue Yi
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan, 610065, China
| | - Dan Zheng
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan, 610065, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan, 610065, China
| | - Yong Nie
- Department of Energy and Resources, College of Engineering, Peking University, Beijing, 100871, China
| | - Bing Hu
- Department of Energy and Resources, College of Engineering, Peking University, Beijing, 100871, China
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan, 610065, China.
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Singh S, Rinta-Kanto JM, Kettunen R, Tolvanen H, Lens P, Collins G, Kokko M, Rintala J. Anaerobic treatment of LCFA-containing synthetic dairy wastewater at 20 °C: Process performance and microbial community dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:960-968. [PMID: 31326818 DOI: 10.1016/j.scitotenv.2019.07.136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/07/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
Facilitating anaerobic degradation of long-chain fatty acids (LCFA) is key for tapping the high methane production potential of the fats, oil and grease (FOG) content of dairy wastewaters. In this study, the feasibility of using high-rate granular sludge reactors for the treatment of mixed LCFA-containing synthetic dairy wastewater (SDW) was assessed at 20 °C. The effects of the LCFA concentration (33-45% of COD) and organic loading rates (2-3 gCOD/L·d) were determined using three parallel expanded granular sludge bed reactors. For the first time, long term anaerobic treatment of LCFA-containing feed at 20 °C was shown to be feasible and was linked to the microbial community dynamics in high-rate reactors. During a two-month operation, a soluble COD removal of 84-91% and COD to methane conversion of 44-51% was obtained. However, granular sludge flotation and washout occurred after two months in all reactors without volatile fatty acids (VFA) accumulation, emphasizing the need for sludge retention for long-term granular sludge reactor operation with LCFA-containing feed at low ambient temperatures. The temporal shifts in microbial community structure were studied in the high-rate treatment of SDW, and the process disturbances (elevated LCFA loading, LCFA accumulation, and batch operation) were found to decrease the microbial community diversity. The relative abundance of Methanosaeta increased with higher LCFA accumulation in the settled and flotation layer granules in the three reactors, therefore, acetoclastic methanogenesis was found to be crucial for the high-rate treatment of SDW at 20 °C. This study provides an initial understanding of the continuous anaerobic treatment of LCFA-containing industrial wastewaters at low ambient temperatures.
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Affiliation(s)
- Suniti Singh
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland.
| | | | - Riitta Kettunen
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland; Tampere Water, Viinikankatu 42 A, 33800 Tampere, Finland.
| | - Henrik Tolvanen
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland.
| | - Piet Lens
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland; UNESCO-IHE Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands.
| | - Gavin Collins
- Microbial Ecophysiology Laboratory, School of Natural Sciences, National University of Ireland, Galway, Ireland.
| | - Marika Kokko
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland.
| | - Jukka Rintala
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland.
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Ziels RM, Nobu MK, Sousa DZ. Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics. mSystems 2019; 4:e00159-19. [PMID: 31387934 PMCID: PMC6687939 DOI: 10.1128/msystems.00159-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/12/2019] [Indexed: 11/20/2022] Open
Abstract
Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after growing on [13C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [13C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling.IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve "who is doing what" by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.
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Affiliation(s)
- Ryan M Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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Acetotrophic Activity Facilitates Methanogenesis from LCFA at Low Temperatures: Screening from Mesophilic Inocula. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2019; 2019:1751783. [PMID: 31191117 PMCID: PMC6525847 DOI: 10.1155/2019/1751783] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/14/2019] [Accepted: 04/03/2019] [Indexed: 12/04/2022]
Abstract
The inoculum source plays a crucial role in the anaerobic treatment of wastewaters. Lipids are present in various wastewaters and have a high methanogenic potential, but their hydrolysis results in the production of long chain fatty acids (LCFAs) that are inhibitory to anaerobic microorganisms. Screening of inoculum for the anaerobic treatment of LCFA-containing wastewaters has been performed at mesophilic and thermophilic conditions. However, an evaluation of inocula for producing methane from LCFA-containing wastewater has not yet been conducted at low temperatures and needs to be undertaken. In this study, three inocula (one granular sludge and two municipal digester sludges) were assessed for methane production from LCFA-containing synthetic dairy wastewater (SDW) at low temperatures (10 and 20°C). A methane yield (based on mL-CH4/g-CODadded) of 86-65% with acetate and 45-20% with SDW was achieved within 10 days using unacclimated granular sludge, whereas the municipal digester sludges produced methane only at 20°C but not at 10°C even after 200 days of incubation. The acetotrophic activity in the inoculum was found to be crucial for methane production from LCFA at low temperatures, highlighting the role of Methanosaeta (acetoclastic archaea) at low temperatures. The presence of bacterial taxa from the family Syntrophaceae (Syntrophus and uncultured taxa) in the inoculum was found to be important for methane production from SDW at 10°C. This study suggests the evaluation of acetotrophic activity and the initial microbial community characteristics by high-throughput amplicon sequencing for selecting the inoculum for producing methane at low temperatures (up to 10°C) from lipid-containing wastewaters.
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Song M, Wang Y, Jiang L, Peng K, Wei Z, Zhang D, Li Y, Zhang G, Luo C. The complex interactions between novel DEHP-metabolising bacteria and the microbes in agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:733-740. [PMID: 30743959 DOI: 10.1016/j.scitotenv.2019.01.052] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/05/2019] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
The indigenous microorganisms with the ability of metabolising di-(2-ethylhexyl) phthalate (DEHP) in agricultural soils and their interactions with non-degrading microbes were revealed by DNA-based stable isotope probing coupled with molecular ecological network. Aside from the previously reported DEHP degraders (family Planococcaceae and genus Sphingobacterium), five OTUs representing bacteria affiliated with genus Brevundimona, class Spartobacteria, genus Singulisphaera, genus Dyella and class Ktedonobacteria were linked with DEHP biodegradation. The analysis of the constructed ecological network based on soil microbial communities demonstrated the negative relationships between DEHP degraders and the dominant family Oxalobacteraceae in soils. Additionally, two cultivable bacteria isolated from the same soils, Rhizobium-1 and Ensifer-1, had strong capabilities in degrading DEHP but their involvement in in situ DEHP degradation was questioned, as their DNA was not labelled with 13C from DEHP. These findings provide deeper understanding on the indigenous DEHP-degrading communities and will benefit the remediation of phthalate esters contaminated soils.
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Affiliation(s)
- Mengke Song
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yujie Wang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Longfei Jiang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Ke Peng
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Zikai Wei
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yongtao Li
- Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Gan Zhang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China.
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Wang J, Liang J, Sun L, Gao S. PVA/CS and PVA/CS/Fe gel beads' synthesis mechanism and their performance in cultivating anaerobic granular sludge. CHEMOSPHERE 2019; 219:130-139. [PMID: 30537586 DOI: 10.1016/j.chemosphere.2018.12.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/14/2018] [Accepted: 12/02/2018] [Indexed: 06/09/2023]
Abstract
Biomass washout from high-speed anaerobic suspended bed bio-reactors is still a challenge to their stable operation. Preserving active biomass to efficiently retain biomass in the reactor is one of the solutions to this problem. Herein, two carriers (polyvinyl alcohol/chitosan (PVA/CS) and PVA/CS/Fe gel beads) were prepared using the cross-linking method. The fourier transform infrared (FTIR) and 13C nuclear magnetic resonance (13C NMR) analyses showed that PVA/CS gel beads formed mainly through hydrogen-bonds (NH2OH-). Furthermore, FTIR, 13C NMR, energy dispersive spectrum (EDS), X-ray diffractometer (XRD) and X-ray photoelectron spectroscopy (XPS) analyses showed that PVA/CS/Fe gel beads formed mainly through chelate bond (NH2-FeM+OH-). The scanning electron microscope (SEM) results affirmed that the gel beads had rough and well-developed porous structure for the attachment of microbes. Furthermore, the abilities of gel beads on the cultivation of granular sludge in an up-flow anaerobic sludge bed (UASB) reactor were effectively demonstrated while treating wastewater polluted with glucose and alkali lignin. The results showed that the gel beads-assisted reactors had a higher performance than those without the gel beads. The cultivation of granules in these reactors was accelerated, while the granules became bigger and exhibited better settling velocities. The reactor with gel beads was easier to withstand a higher organic loading rate due to dense microbial aggregates, which were caused by more humic-like substance. Particularly, the reactor with PVA/CS/Fe gel beads was able to improve the overall robustness of the system due to stronger mechanical properties of gel beads, and also prevented cells detachment.
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Affiliation(s)
- Jinxing Wang
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jidong Liang
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Li Sun
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Sha Gao
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China
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Teng Y, Xu Y, Wang X, Christie P. Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation. Front Microbiol 2019; 10:106. [PMID: 30837956 PMCID: PMC6383490 DOI: 10.3389/fmicb.2019.00106] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/17/2019] [Indexed: 01/30/2023] Open
Abstract
Hydrogen (H2) metabolism has attracted considerable interest because the activities of H2-producing and consuming microbes shape the global H2 cycle and may have vital relationships with the global cycling of other elements. There are many pathways of microbial H2 emission and consumption which may affect the structure and function of microbial communities. A wide range of microbial groups employ H2 as an electron donor to catalyze the reduction of pollutants such as organohalides, azo compounds, and trace metals. Syntrophy coupled mutualistic interaction between H2-producing and H2-consuming microorganisms can transfer H2 and be accompanied by the removal of toxic compounds. Moreover, hydrogenases have been gradually recognized to have a key role in the progress of pollutant degradation. This paper reviews recent advances in elucidating role of H2 metabolism involved in syntrophy and hydrogenases in environmental bioremediation. Further investigations should focus on the application of bioenergy in bioremediation to make microbiological H2 metabolism a promising remediation strategy.
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Affiliation(s)
- Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Inhibition Studies with 2-Bromoethanesulfonate Reveal a Novel Syntrophic Relationship in Anaerobic Oleate Degradation. Appl Environ Microbiol 2019; 85:AEM.01733-18. [PMID: 30366998 PMCID: PMC6328780 DOI: 10.1128/aem.01733-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/23/2018] [Indexed: 12/25/2022] Open
Abstract
In anaerobic treatment of complex wastewater containing fat, oils, and grease, high long-chain fatty acid (LCFA) concentrations may inhibit microbial communities, particularly those of methanogens. Here, we investigated if anaerobic degradation of LCFAs can proceed when methanogens are inhibited and in the absence of typical external electron acceptors, such as nitrate, iron, or sulfate. Inhibition studies were performed with the methanogenic inhibitor 2-bromoethanesulfonate (BrES). We noticed that, after autoclaving, BrES underwent partial hydrolysis and turned out to be a mixture of two sulfonates (BrES and isethionate). We found out that LCFA conversion proceeded faster in the assays where methanogenesis was inhibited, and that it was dependent on the utilization of isethionate. In this study, we report LCFA degradation coupled to desulfonation. Our results also showed that BrES can be utilized by anaerobic bacteria. Degradation of long-chain fatty acids (LCFAs) in methanogenic environments is a syntrophic process involving the activity of LCFA-degrading bacteria and hydrogen-utilizing methanogens. If methanogens are inhibited, other hydrogen scavengers are needed to achieve complete LCFA degradation. In this work, we developed two different oleate (C18:1 LCFA)-degrading anaerobic enrichment cultures, one methanogenic (ME) and another in which methanogenesis was inhibited (IE). Inhibition of methanogens was attained by adding a solution of 2-bromoethanesulfonate (BrES), which turned out to consist of a mixture of BrES and isethionate. Approximately 5 times faster oleate degradation was accomplished by the IE culture compared with the ME culture. A bacterium closely related to Syntrophomonas zehnderi (99% 16S rRNA gene identity) was the main oleate degrader in both enrichments, in syntrophic relationship with hydrogenotrophic methanogens from the genera Methanobacterium and Methanoculleus (in ME culture) or with a bacterium closely related to Desulfovibrio aminophilus (in IE culture). A Desulfovibrio species was isolated, and its ability to utilize hydrogen was confirmed. This bacterium converted isethionate to acetate and sulfide, with or without hydrogen as electron donor. This bacterium also utilized BrES but only after 3 months of incubation. Our study shows that syntrophic oleate degradation can be coupled to desulfonation. IMPORTANCE In anaerobic treatment of complex wastewater containing fat, oils, and grease, high long-chain fatty acid (LCFA) concentrations may inhibit microbial communities, particularly those of methanogens. Here, we investigated if anaerobic degradation of LCFAs can proceed when methanogens are inhibited and in the absence of typical external electron acceptors, such as nitrate, iron, or sulfate. Inhibition studies were performed with the methanogenic inhibitor 2-bromoethanesulfonate (BrES). We noticed that, after autoclaving, BrES underwent partial hydrolysis and turned out to be a mixture of two sulfonates (BrES and isethionate). We found out that LCFA conversion proceeded faster in the assays where methanogenesis was inhibited, and that it was dependent on the utilization of isethionate. In this study, we report LCFA degradation coupled to desulfonation. Our results also showed that BrES can be utilized by anaerobic bacteria.
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