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Liu N, Kivenson V, Peng X, Cui Z, Lankiewicz TS, Gosselin KM, English CJ, Blair EM, O'Malley MA, Valentine DL. Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen. Appl Environ Microbiol 2024; 90:e0091423. [PMID: 38265213 PMCID: PMC10880615 DOI: 10.1128/aem.00914-23] [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] [Received: 06/07/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.
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Affiliation(s)
- Na Liu
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Veronika Kivenson
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Xuefeng Peng
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, China
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Kelsey M. Gosselin
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chance J. English
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Ecology Evolution, and Marine Biology, University of California, Santa Barbara, California, USA
| | - Elaina M. Blair
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
- Biological Engineering Program, University of California, Santa Barbara, California, USA
| | - David L. Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, California, USA
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Zhang YS, Zhang YQ, Zhao XM, Liu XL, Qin QL, Liu NH, Xu F, Chen XL, Zhang YZ, Li PY. Metagenomic insights into the dynamic degradation of brown algal polysaccharides by kelp-associated microbiota. Appl Environ Microbiol 2024; 90:e0202523. [PMID: 38259074 PMCID: PMC10880675 DOI: 10.1128/aem.02025-23] [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] [Received: 11/12/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Marine bacteria play important roles in the degradation and cycling of algal polysaccharides. However, the dynamics of epiphytic bacterial communities and their roles in algal polysaccharide degradation during kelp decay are still unclear. Here, we performed metagenomic analyses to investigate the identities and predicted metabolic abilities of epiphytic bacterial communities during the early and late decay stages of the kelp Saccharina japonica. During kelp decay, the dominant epiphytic bacterial communities shifted from Gammaproteobacteria to Verrucomicrobia and Bacteroidetes. In the early decay stage of S. japonica, epiphytic bacteria primarily targeted kelp-derived labile alginate for degradation, among which the gammaproteobacterial Vibrionaceae (particularly Vibrio) and Psychromonadaceae (particularly Psychromonas), abundant in alginate lyases belonging to the polysaccharide lyase (PL) families PL6, PL7, and PL17, were key alginate degraders. More complex fucoidan was preferred to be degraded in the late decay stage of S. japonica by epiphytic bacteria, predominantly from Verrucomicrobia (particularly Lentimonas), Pirellulaceae of Planctomycetes (particularly Rhodopirellula), Pontiellaceae of Kiritimatiellota, and Flavobacteriaceae of Bacteroidetes, which depended on using glycoside hydrolases (GHs) from the GH29, GH95, and GH141 families and sulfatases from the S1_15, S1_16, S1_17, and S1_25 families to depolymerize fucoidan. The pathways for algal polysaccharide degradation in dominant epiphytic bacterial groups were reconstructed based on analyses of metagenome-assembled genomes. This study sheds light on the roles of different epiphytic bacteria in the degradation of brown algal polysaccharides.IMPORTANCEKelps are important primary producers in coastal marine ecosystems. Polysaccharides, as major components of brown algal biomass, constitute a large fraction of organic carbon in the ocean. However, knowledge of the identities and pathways of epiphytic bacteria involved in the degradation process of brown algal polysaccharides during kelp decay is still elusive. Here, based on metagenomic analyses, the succession of epiphytic bacterial communities and their metabolic potential were investigated during the early and late decay stages of Saccharina japonica. Our study revealed a transition in algal polysaccharide-degrading bacteria during kelp decay, shifting from alginate-degrading Gammaproteobacteria to fucoidan-degrading Verrucomicrobia, Planctomycetes, Kiritimatiellota, and Bacteroidetes. A model for the dynamic degradation of algal cell wall polysaccharides, a complex organic carbon, by epiphytic microbiota during kelp decay was proposed. This study deepens our understanding of the role of epiphytic bacteria in marine algal carbon cycling as well as pathogen control in algal culture.
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Affiliation(s)
- Yi-Shuo Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Qi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiang-Ming Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Lei Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Joint Research Center for Marine Microbiol Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Joint Research Center for Marine Microbiol Science and Technology, Shandong University and Ocean University of China, Qingdao, China
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Gao Q, He J, Wang J, Yan Y, Liu L, Wang Z, Shen W, Wan F. Effects of dietary D-lactate levels on rumen fermentation, microflora and metabolomics of beef cattle. Front Microbiol 2024; 15:1348729. [PMID: 38380091 PMCID: PMC10877051 DOI: 10.3389/fmicb.2024.1348729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Introduction Excessive intake of lactate caused by improper use of silage in animal husbandry has adverse effects on rumen fermentation, such as rumen acidosis. The speed of absorption and metabolism of D-lactate in rumen epithelial cells was slower than that of L-lactate, making D-lactate more prone to accumulate and induce rumen acidosis. Therefore, this study was conducted to explore the effects of dietary D-lactate levels on rumen fermentation of beef cattle and its mechanism in an in vitro system. Methods This experiment was adopted in single-factor random trial design, with 5 days for adaptation and 3 days for sample collection. Three treatments (n = 8/treatment) were used: (1) D-LA (0.3%), basal fermentation substrate with 0.3% (dry matter, DM basis) D-lactate; (2) D-LA (0.75%), basal fermentation substrate with 0.75% (DM basis) D-lactate; and (3) D-LA (1.2%), basal fermentation substrate with 1.2% (DM basis) D-lactate. Results With the dietary D-lactate levels increased, the daily production of total gas, hydrogen and methane, as well as the ruminal concentrations of acetate, propionate, butyrate, isobutyrate, valerate, isovalerate, total volatile fatty acid and D-lactate increased (p < 0.05), but the ruminal pH and acetate/propionate ratios decreased (p < 0.05). Principle coordinate analysis based on Bray-Curtis distance showed that increasing dietary D-lactate levels could significantly affect the structure of rumen bacterial community (p < 0.05), but had no significant effect on the structure of rumen eukaryotic community (p > 0.05). NK4A214_group, Ruminococcus_gauvreauii_group, Eubacterium_oxidoreducens_group, Escherichia-Shigella, Marvinbryantia and Entodinium were enriched in D-LA (1.2%) group (p < 0.05), as well as WCHB1-41, vadinBE97, Clostridium_sensu_stricto_1, Anaeroplasma and Ruminococcus were enriched in D-LA (0.3%) group (p < 0.05). Changes in the composition of ruminal microorganisms affected rumen metabolism, mainly focus on the biosynthesis of glycosaminoglycans (p < 0.05). Discussion Overall, feeding whole-plant corn silage with high D-lactate content could not induce rumen acidosis, and the metabolization of dietary D-lactate into volatile fatty acids increased the energy supply of beef cattle. However, it also increased the ruminal CH4 emissions and the relative abundance of opportunistic pathogen Escherichia-Shigella in beef cattle. The relative abundance of Verrucomicrobiota and Escherichia-Shigella may be influenced by glycosaminoglycans, reflecting the interaction between rumen microorganisms and metabolites.
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Affiliation(s)
- Qian Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jianfu He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jin Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Yonghui Yan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Lei Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China
| | - Zuo Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Weijun Shen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Fachun Wan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
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Gong T, Di H, Hu Y, Xu S, Chen J, Chen G, Wei X, Liu C. Gut microbiota and metabolites exhibit different profiles after very-low-caloric restriction in patients with type 2 diabetes. Front Endocrinol (Lausanne) 2024; 14:1289571. [PMID: 38269247 PMCID: PMC10807290 DOI: 10.3389/fendo.2023.1289571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/11/2023] [Indexed: 01/26/2024] Open
Abstract
Background and aims To investigate the effect of short-term very-low-calorie restriction (VLCR) on metabolism in patients with type 2 diabetes (T2D), and elucidate the molecular mechanism through analyses on gut microbiota and small-molecule metabolites. Methods Fourteen T2D patients were hospitalized to receive VLCR (300-600 kcal/d) for 9 days. BMI, BP, and HR were taken before and after VLCR. Levels of blood lipids, fasting insulin, FBG, and 2h PBG were assessed. The microbial diversity in feces was detected by 16S rDNA high-throughput sequencing technology, and small-molecule metabolites in plasma and feces by untargeted metabolomics technology. Results After VLCR, BW, BMI, WC, BP, and levels of FBG and 2h PBG, insulin, HOMA-IR, and triglyceride decreased significantly in T2D patients (P<0.05). There was no significant change in the α-diversity of fecal microbiota, but the abundance of Bacteroidetes increased significantly, and the Firmicutes/Bacteroidetes ratio decreased significantly from 11.79 to 4.20. Parabacteroides distasonis showed an abundance having increased most prominently after VLCR treatment. Plasma level of amino acid metabolite L-arginine increased significantly. Plasma levels of three lipid metabolites, PC (14:0/20:4 [8Z, 11Z, 14Z, 17Z]), LysoPC (16:1 [9Z]) and LysoPC (18:1 [11Z]), were significantly reduced. Fecal levels of lipid metabolite LysoPC (18:1 [11Z]) and bile acid metabolite glycholic acid were significantly decreased. Conclusion In T2DM patients, VLCR can considerably reduce body weight and improve glucose and lipid metabolism without causing severe side effects. LysoPC (18:1 [11Z]) and Parabacteroides distasonis showed the most obvious difference after VLCR, which could be the indicators for VLCR in T2D.
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Affiliation(s)
- Tong Gong
- Department of Endocrinology, Jiangsu Province Second Hospital of Chinese Medicine, Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongjie Di
- Department of Endocrinology, Jiangsu Province Second Hospital of Chinese Medicine, Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yongxin Hu
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Shuhang Xu
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Jie Chen
- Department of Nutrition, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guofang Chen
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Xiao Wei
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Chao Liu
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
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Oliver A, Podell S, Kelly LW, Sparagon WJ, Plominsky AM, Nelson RS, Laurens LML, Augyte S, Sims NA, Nelson CE, Allen EE. Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.568905. [PMID: 38076955 PMCID: PMC10705383 DOI: 10.1101/2023.11.28.568905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce foundational genomic work on the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzymes able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) suggest the potential for microbial transfer between marine sediment and Kyphosus digestive tracts. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.
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Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Wesley J. Sparagon
- Daniel K. Inouye Center for Microbial Oceanography, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - Alvaro M. Plominsky
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | - Craig E. Nelson
- Daniel K. Inouye Center for Microbial Oceanography, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - Eric E. Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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Wang M, Zheng N, Li X, Zhao K, Xie BB. Enrichment Pretreatment Expands the Microbial Diversity Cultivated from Marine Sediments. Microorganisms 2023; 11:2771. [PMID: 38004782 PMCID: PMC10673404 DOI: 10.3390/microorganisms11112771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The majority of the microbial diversity in nature has not been recovered through cultivation. Enrichment is a classical technique widely used in the selective cultivation of specific taxa. Whether enrichment is suitable for cultivation studies that aim to recover large numbers of species remains little explored. To address this issue, we evaluated the potential of enrichment pretreatment in the cultivation of bacteria from marine sediments. Upon obtaining and classifying a total of 943 pure cultures from chitin and cellulose enrichment pretreatment systems and a control system, our results showed that species obtained using enrichment pretreatment differed greatly from those without enrichment. Multiple enrichment media and different enrichment times increased the number of cultivated species in a sample. Amplicon sequencing showed that the increased relative abundance during pretreatment contributed greatly to bacterial cultivation. The testing of degradation abilities against chitin and cellulose and the whole-genome sequencing of representative strains suggested that microorganism-microorganism interactions play roles in the expanded diversity of cultivated bacteria. This study provides new insights into the abilities of enrichment in exploring cultivable diversity and mining microbial resources.
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Affiliation(s)
| | | | | | | | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.W.); (N.Z.); (X.L.); (K.Z.)
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Cabrol L, Capo E, van Vliet DM, von Meijenfeldt FAB, Bertilsson S, Villanueva L, Sánchez-Andrea I, Björn E, G. Bravo A, Heimburger Boavida LE. Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea. mSystems 2023; 8:e0053723. [PMID: 37578240 PMCID: PMC10469668 DOI: 10.1128/msystems.00537-23] [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] [Received: 05/24/2023] [Accepted: 06/16/2023] [Indexed: 08/15/2023] Open
Abstract
In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc+) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc+ microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc+ microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc+) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc+ microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.
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Affiliation(s)
- Léa Cabrol
- Aix Marseille University, Univ. Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
- Institute of Ecology and Biodiversity (IEB), University of Chile, Santiago, Chile
| | - Eric Capo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Daan M. van Vliet
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
- Wageningen Food and Biobased Research, Wageningen, the Netherlands
| | - F. A. Bastiaan von Meijenfeldt
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Erik Björn
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Andrea G. Bravo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain
| | - Lars-Eric Heimburger Boavida
- Aix Marseille University, Univ. Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
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Yao H, Liu S, Liu T, Ren D, Yang Q, Zhou Z, Mao J. Screening of marine sediment-derived microorganisms and their bioactive metabolites: a review. World J Microbiol Biotechnol 2023; 39:172. [PMID: 37115432 DOI: 10.1007/s11274-023-03621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
Marine sediments are one of the largest habitats on Earth, and their unique ecology, such as high salinity, high pressure, and hypoxia, may activate certain silent genes in marine microbes, resulting in microbes, enzymes, active products, and specific metabolic pathways that can adapt to these specific ecological environments. Marine sediment-derived microorganisms and their bioactive metabolites are of great significance and have potential commercial development prospects for food, pharmaceutical, chemical industries, agriculture, environmental protection and human nutrition and health. In recent years, although there have been numerous scientific reports surrounding marine sediment-derived microorganisms and their bioactive metabolites, a comprehensive review of their research progress is lacking. This paper presents the development and renewal of traditional culture-dependent and omics analysis techniques and their application to the screening of marine sediment-derived microorganisms producing bioactive substances. It also highlights recent research advances in the last five years surrounding the types, functional properties and potential applications of bioactive metabolites produced by marine sediment-derived microorganisms. These bioactive metabolites mainly include antibiotics, enzymes, enzyme inhibitors, sugars, proteins, peptides, and some other small molecule metabolites. In addition, the review ends with concluding remarks on the challenges and future directions for marine sediment-derived microorganisms and their bioactive metabolites. The review report not only helps to deepen the understanding of marine sediment-derived microorganisms and their bioactive metabolites, but also provides some useful information for the exploitation and utilization of marine microbial resources and the mining of new compounds with potential functional properties.
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Affiliation(s)
- Hongli Yao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Department of Biology and Food Engineering, Bozhou University, Bozhou, 236800, Anhui, China
| | - Shuangping Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Tiantian Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Dongliang Ren
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qilin Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhilei Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Jian Mao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China.
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China.
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9
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Dionisi HM, Lozada M, Campos E. Diversity of GH51 α-L-arabinofuranosidase homolog sequences from subantarctic intertidal sediments. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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10
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Lozada M, Diéguez MC, García PE, Dionisi HM. Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159392. [PMID: 36240919 DOI: 10.1016/j.scitotenv.2022.159392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Kelp forests, among the most productive ecosystems on Earth, cover large areas of the South Atlantic coast. Sediment heterotrophic bacteria have a pivotal role in the degradation of kelp biomass, however, the response of sediment microbial communities to periodic kelp biomass inputs is mostly unknown. Here, we show that kelp biomass induced rapid changes in overlying water chemistry and shifts in sediment microbial communities, which differed in the experimental systems containing Macrocystis pyrifera (M) and Undaria pinnatifida (U) with sediments of the respective regions. We observed results compatible with the degradation of labile, high molecular weight compounds into smaller and more refractory compounds towards the end of the incubations. The capability of microbial communities to degrade alginate, the major component of kelp cell walls, significantly increased with respect to controls after kelp biomass addition (Absorbance at 235 nm 1.2 ± 0.3 and 1.0 ± 0.2 for M and U, respectively, controls <0.2, t = 4 days). Shifts in microbial community structure (based on 16S rRNA gene amplicon sequencing) were tightly related to the kelp treatment and, to a lesser extent, to the sediment provenance (Principal Coordinates Analysis, 80 % of variation explained in the first two axes). Dissolved oxygen, pH, salinity, alginolytic potential, Absorbance at 235 and 600 nm, total N, total C, and SUVA index correlated significantly with community structure. Differentially abundant populations between kelp-amended treatments and controls included members of the Flavobacteriia class (Algibacter and Polaribacter), and Gammaproteobacteria (Psychromonas and Marinomonas), among others. Metagenomes of M and U-amended sediments contained sequences from 18 of the 19 enzyme families related to alginate or fucoidan degradation. Specific taxonomic groups were associated with enzyme classes targeting different substrates, suggesting niche differentiation. This work expands our knowledge on the patterns of microbial assemblages from intertidal sediments in response to kelp biomass inputs.
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Affiliation(s)
- Mariana Lozada
- Laboratorio de Microbiología Ambiental (CESIMAR-CONICET/IBIOMAR-CONICET), Puerto Madryn, Argentina.
| | - María C Diéguez
- Grupo de Ecología de Sistemas Acuáticos a Escala de Paisaje (GESAP, INIBIOMA-CONICET-UNComa), Bariloche, Argentina
| | - Patricia E García
- Grupo de Ecología de Sistemas Acuáticos a Escala de Paisaje (GESAP, INIBIOMA-CONICET-UNComa), Bariloche, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental (CESIMAR-CONICET/IBIOMAR-CONICET), Puerto Madryn, Argentina
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11
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Bioprospecting for Novel Bacterial Sources of Hydrolytic Enzymes and Antimicrobials in the Romanian Littoral Zone of the Black Sea. Microorganisms 2022; 10:microorganisms10122468. [PMID: 36557721 PMCID: PMC9780896 DOI: 10.3390/microorganisms10122468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Marine microorganisms have evolved a large variety of metabolites and biochemical processes, providing great opportunities for biotechnologies. In the search for new hydrolytic enzymes and antimicrobial compounds with enhanced characteristics, the current study explored the diversity of cultured and uncultured marine bacteria in Black Sea water from two locations along the Romanian coastline. Microbial cell density in the investigated samples varied between 65 and 12.7 × 103 CFU·mL-1. The total bacterial community identified by Illumina sequencing of 16S rRNA gene comprised 185 genera belonging to 46 classes, mainly Gammaproteobacteria, Alphaproteobacteria, Flavobacteriia, and 24 phyla. The 66 bacterial strains isolated on seawater-based culture media belonged to 33 genera and showed variable growth temperatures, growth rates, and salt tolerance. A great fraction of these strains, including Pseudoalteromonas and Flavobacterium species, produced extracellular proteases, lipases, and carbohydrases, while two strains belonging to the genera Aquimarina and Streptomyces exhibited antimicrobial activity against human pathogenic bacteria. This study led to a broader view on the diversity of microbial communities in the Black Sea, and provided new marine strains with hydrolytic and antimicrobial capabilities that may be exploited in industrial and pharmaceutical applications.
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12
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Skoog EJ, Moore KR, Gong J, Ciccarese D, Momper L, Cutts EM, Bosak T. Metagenomic, (bio)chemical, and microscopic analyses reveal the potential for the cycling of sulfated EPS in Shark Bay pustular mats. ISME COMMUNICATIONS 2022; 2:43. [PMID: 37938726 PMCID: PMC9723792 DOI: 10.1038/s43705-022-00128-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/12/2022] [Accepted: 04/27/2022] [Indexed: 05/24/2023]
Abstract
Cyanobacteria and extracellular polymeric substances (EPS) in peritidal pustular microbial mats have a two-billion-year-old fossil record. To understand the composition, production, degradation, and potential role of EPS in modern analogous communities, we sampled pustular mats from Shark Bay, Australia and analyzed their EPS matrix. Biochemical and microscopic analyses identified sulfated organic compounds as major components of mat EPS. Sulfur was more abundant in the unmineralized regions with cyanobacteria and less prevalent in areas that contained fewer cyanobacteria and more carbonate precipitates. Sequencing and assembly of the pustular mat sample resulted in 83 high-quality metagenome-assembled genomes (MAGs). Metagenomic analyses confirmed cyanobacteria as the primary sources of these sulfated polysaccharides. Genes encoding for sulfatases, glycosyl hydrolases, and other enzymes with predicted roles in the degradation of sulfated polysaccharides were detected in the MAGs of numerous clades including Bacteroidetes, Chloroflexi, Hydrogenedentes, Myxococcota, Verrucomicrobia, and Planctomycetes. Measurable sulfatase activity in pustular mats and fresh cyanobacterial EPS confirmed the role of sulfatases in the degradation of sulfated EPS. These findings suggest that the synthesis, modification, and degradation of sulfated polysaccharides influence microbial interactions, carbon cycling, and biomineralization processes within peritidal pustular microbial mats.
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Affiliation(s)
- Emilie J Skoog
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Kelsey R Moore
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- California Institute of Technology, Division of Geological and Planetary Sciences, Pasadena, CA, 91125, USA
| | - Jian Gong
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Davide Ciccarese
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lily Momper
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Exponent, Inc., Pasadena, CA, 91106, USA
| | - Elise M Cutts
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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13
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Hettle AG, Vickers CJ, Boraston AB. Sulfatases: Critical Enzymes for Algal Polysaccharide Processing. FRONTIERS IN PLANT SCIENCE 2022; 13:837636. [PMID: 35574087 PMCID: PMC9096561 DOI: 10.3389/fpls.2022.837636] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Microbial sulfatases are important biocatalysts in the marine environment where they play a key role in the catabolic biotransformation of abundant sulphated algal polysaccharides. The sulphate esters decorating algal polysaccharides, such as carrageenan, fucoidan and ulvan, can constitute up to 40% of the biopolymer dry weight. The use of this plentiful carbon and energy source by heterotrophic microbes is enabled in part by the sulfatases encoded in their genomes. Sulfatase catalysed hydrolytic removal of sulphate esters is a key reaction at various stages of the enzymatic cascade that depolymerises sulphated polysaccharides into monosaccharides that can enter energy yielding metabolic pathways. As the critical roles of sulfatases in the metabolism of sulphated polysaccharides from marine algae is increasingly revealed, the structural and functional analysis of these enzymes becomes an important component of understanding these metabolic pathways. The S1 family of formylglycine-dependent sulfatases is the largest and most functionally diverse sulfatase family that is frequently active on polysaccharides. Here, we review this important sulfatase family with emphasis on recent developments in studying the structural and functional relationship between sulfatases and their sulphated algal polysaccharide substrates. This analysis utilises the recently proposed active site nomenclature for sulfatases. We will highlight the key role of sulfatases, not only in marine carbon cycling, but also as potential biocatalysts for the production of a variety of novel tailor made sulphated oligomers, which are useful products in, for example, pharmaceutical or cosmetic applications.
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Affiliation(s)
- Andrew G. Hettle
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Chelsea J. Vickers
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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14
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Williams TJ, Allen MA, Panwar P, Cavicchioli R. Into the darkness: The ecologies of novel 'microbial dark matter' phyla in an Antarctic lake. Environ Microbiol 2022; 24:2576-2603. [PMID: 35466505 PMCID: PMC9324843 DOI: 10.1111/1462-2920.16026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022]
Abstract
Uncultivated microbial clades ("microbial dark matter") are inferred to play important, but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome-assembled genomes (MAGs; 88-100% complete) were generated for four "dark matter" phyla: six MAGs from Candidatus Auribacterota (= Aureabacteria, SURF-CP-2), inferred to be hydrogen- and sulfide-producing fermentative heterotrophs, with individual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili; one MAG (100% complete) from Candidatus Hinthialibacterota (= OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g., sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili; three MAGs from Candidatus Electryoneota (= AABM5-125-24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes; two MAGs from Candidatus Lernaellota (= FEN-1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88-100% identity) suggests these "dark matter" phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautrophic CO2 fixation in diverse global environments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences UNSW Sydney, Sydney, New South Wales, 2052, Australia
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15
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Huang W, Tan H, Nie S. Beneficial effects of seaweed-derived dietary fiber: Highlights of the sulfated polysaccharides. Food Chem 2022; 373:131608. [PMID: 34815114 DOI: 10.1016/j.foodchem.2021.131608] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022]
Abstract
Seaweeds and their derivatives are important bioresources of natural bioactive compounds. Nutritional studies indicate that dietary fibers derived from seaweeds have great beneficial potentials in human health and can be developed as functional food. Moreover, sulfated polysaccharides are more likely to be the main bioactive components which are widely distributed in various species of seaweeds including Phaeophyceae, Rhodophyceae and Chlorophyceae. The catabolism by gut microbiota of the seaweeds-derived dietary fibers (DFs) may be one of the pivotal pathways of their physiological functions. Therefore, in this review, we summarized the latest results of the physiological characteristics of seaweed-derived dietary fiber and highlighted the roles of sulfated polysaccharides in the potential regulatory mechanisms against disorders. Meanwhile, the effects of different types of seaweed-derived dietary fiber on gut microbiota were discussed. The analysis of the structure-function correlations and gut microbiota related mechanisms and will contribute to further better applications in food and biotherapeutics.
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Affiliation(s)
- Wenqi Huang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Huizi Tan
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
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16
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Fiard M, Cuny P, Sylvi L, Hubas C, Jézéquel R, Lamy D, Walcker R, El Houssainy A, Heimbürger-Boavida LE, Robinet T, Bihannic I, Gilbert F, Michaud E, Dirberg G, Militon C. Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150667. [PMID: 34599952 DOI: 10.1016/j.scitotenv.2021.150667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cédric Hubas
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Dominique Lamy
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France; Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), Sorbonne Université, Univ Paris Est Créteil, IRD, CNRS, INRA, 4 place Jussieu, 75005 Paris, France.
| | - Romain Walcker
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Amonda El Houssainy
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | | | - Tony Robinet
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Franck Gilbert
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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17
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Flood BE, Louw DC, Van der Plas AK, Bailey JV. Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes. PLoS One 2021; 16:e0258124. [PMID: 34818329 PMCID: PMC8612568 DOI: 10.1371/journal.pone.0258124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H2 and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.
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Affiliation(s)
- Beverly E. Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail:
| | - Deon C. Louw
- National Marine Information and Research Centre, Swakopmund, Namibia
| | | | - Jake V. Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Twin Cities, Minnesota, United States of America
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18
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Campbell MA, Coolen MJL, Visscher PT, Morris T, Grice K. Structure and function of Shark Bay microbial communities following tropical cyclone Olwyn: A metatranscriptomic and organic geochemical perspective. GEOBIOLOGY 2021; 19:642-664. [PMID: 34180124 DOI: 10.1111/gbi.12461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/05/2021] [Indexed: 06/13/2023]
Abstract
Shark Bay, Western Australia, is episodically impacted by tropical cyclones. During 2015, the region was hit by a category 3 cyclone, "severe tropical cyclone Olywn," leading to the formation of a black sludge in an intertidal zone harboring microbial mats and microbialites. Upon returning to the impacted site 12 months later, the black sludge deposit was still recognizable between the microbialite columns and mucilaginous cobbles near the shoreline in the impacted area. Metatranscriptomic and organic geochemical analyses were carried out on the cyclone-derived materials and impacted microbial mat communities to unravel the structure, function, and potential preservation of these deposits following a tropical cyclone. It was found that samples derived from the black sludge contained low relative abundances of cyanobacteria but had higher proportions of heterotrophic and anaerobic microorganisms (e.g., methanogens and sulfate-reducing bacteria). Increased metabolic activity by these microorganisms (e.g., sulfate reduction and organic matter degradation) is thought to drive calcium carbonate precipitation and helps in mat preservation. Comparison of the aliphatic biomarker by gas chromatography-mass spectrometry (GC-MS) analyses showed that C25 highly branched isoprenoid (HBI) alkenes were significantly higher in the cyclone-derived materials attributed to the relocation of subtidal sediments containing HBI-producing diatom communities by the tropical cyclone. Raney nickel desulfurization of the polar fraction extracted from a mucilaginous cobble revealed sulfur-bound hopanoids and a series of benzohopanes. The presence of these compounds could be indicative of microbial matter that has been influenced by the tropical cyclone which may have caused elevated levels of water column anoxia promoting increased sulfurization of the organic matter to occur.
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Affiliation(s)
- Matthew A Campbell
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Marco J L Coolen
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Pieter T Visscher
- Departments of Marine Sciences and Geoscience, University of Connecticut, Storrs, CT, USA
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Therese Morris
- Applied Geology, Curtin University, Perth, WA, Australia
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
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19
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Boey JS, Mortimer R, Couturier A, Worrallo K, Handley KM. Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance. Environ Microbiol 2021; 24:50-65. [PMID: 33973326 DOI: 10.1111/1462-2920.15550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/22/2023]
Abstract
Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N2 O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N2 O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.
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Affiliation(s)
- Jian Sheng Boey
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Redmond Mortimer
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Agathe Couturier
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.,Ecole Supérieure de Biologie Biochimie Biotechnologies, Faculté des Sciences, Université Catholique de Lyon, Lyon, France
| | - Katie Worrallo
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Kim M Handley
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
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20
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Mu DS, Ouyang Y, Chen GJ, Du ZJ. Strategies for culturing active/dormant marine microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:121-131. [PMID: 37073338 PMCID: PMC10077298 DOI: 10.1007/s42995-020-00053-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/18/2020] [Indexed: 05/03/2023]
Abstract
Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However, many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture, there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for 'unculturable microbes' and categorizes uncultured bacteria into three groups: dominant active bacteria, rare active bacteria, and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria. Simulating the natural environment is an effective strategy for isolating dominant active bacteria, whereas culturomics and enrichment culture methods are proposed for isolating rare active bacteria. For dormant bacteria, resuscitation culture is an appropriate strategy. Furthermore, the review provides a list of the most-wanted bacteria and proposes potential strategies for culturing these bacteria in marine environments. The review provides new insight into the development of strategies for the cultivation of specific groups of uncultured bacteria and therefore paves the way for the detection of novel microbes and their functions in marine ecosystems.
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Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Marine College, Shandong University, Weihai, 264209 China
| | - Yang Ouyang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK USA
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Marine College, Shandong University, Weihai, 264209 China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Marine College, Shandong University, Weihai, 264209 China
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21
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Undaria pinnatifida exudates trigger shifts in seawater chemistry and microbial communities from Atlantic Patagonian coasts. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02471-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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22
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Borchert E, García-Moyano A, Sanchez-Carrillo S, Dahlgren TG, Slaby BM, Bjerga GEK, Ferrer M, Franzenburg S, Hentschel U. Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort. mSystems 2021; 6:e01218-20. [PMID: 33563781 PMCID: PMC7883544 DOI: 10.1128/msystems.01218-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/20/2021] [Indexed: 11/29/2022] Open
Abstract
The marine bone biome is a complex assemblage of macro- and microorganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic collagen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of microbial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia contained the most diverse gene repertoires. We postulate that demineralization of inorganic bone components is achieved by a timely succession of a closed sulfur biogeochemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone surface communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia IMPORTANCE Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment. We here demonstrate the interplay between different bacterial community members, each supplying different enzymatic functions with the potential to cover an array of reactions relating to the degradation of bone matrix components. We identify and describe a novel gene cluster for collagen utilization, which is a key function in this unique environment. We propose that the interplay between the different microbial taxa is necessary to achieve the complex task of bone degradation in the marine environment.
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Affiliation(s)
- Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | | | | | - Thomas G Dahlgren
- NORCE Norwegian Research Centre, Bergen, Norway
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Beate M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | | | | | - Sören Franzenburg
- IKMB, Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
- Christian-Albrechts University of Kiel, Kiel, Germany
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23
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Peterson BD, McDaniel EA, Schmidt AG, Lepak RF, Janssen SE, Tran PQ, Marick RA, Ogorek JM, DeWild JF, Krabbenhoft DP, McMahon KD. Mercury Methylation Genes Identified across Diverse Anaerobic Microbial Guilds in a Eutrophic Sulfate-Enriched Lake. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15840-15851. [PMID: 33228362 PMCID: PMC9741811 DOI: 10.1021/acs.est.0c05435] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Mercury (Hg) methylation is a microbially mediated process that converts inorganic Hg into bioaccumulative, neurotoxic methylmercury (MeHg). The metabolic activity of methylating organisms is highly dependent on biogeochemical conditions, which subsequently influences MeHg production. However, our understanding of the ecophysiology of methylators in natural ecosystems is still limited. Here, we identified potential locations of MeHg production in the anoxic, sulfidic hypolimnion of a freshwater lake. At these sites, we used shotgun metagenomics to characterize microorganisms with the Hg-methylation gene hgcA. Putative methylators were dominated by hgcA sequences divergent from those in well-studied, confirmed methylators. Using genome-resolved metagenomics, we identified organisms with hgcA (hgcA+) within the Bacteroidetes and the recently described Kiritimatiellaeota phyla. We identified hgcA+ genomes derived from sulfate-reducing bacteria, but these accounted for only 22% of hgcA+ genome coverage. The most abundant hgcA+ genomes were from fermenters, accounting for over half of the hgcA gene coverage. Many of these organisms also mediate hydrolysis of polysaccharides, likely from cyanobacterial blooms. This work highlights the distribution of the Hg-methylation genes across microbial metabolic guilds and indicate that primary degradation of polysaccharides and fermentation may play an important but unrecognized role in MeHg production in the anoxic hypolimnion of freshwater lakes.
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Affiliation(s)
- Benjamin D. Peterson
- Environmental Science & Technology Program, University of Wisconsin - Madison, 660 N. Park Street, Madison, WI 53706, USA
- Corresponding author:
| | - Elizabeth A. McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Anna G. Schmidt
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Ryan F. Lepak
- Environmental Science & Technology Program, University of Wisconsin - Madison, 660 N. Park Street, Madison, WI 53706, USA
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
- U.S. Environmental Protection Agency Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Sarah E. Janssen
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - Patricia Q. Tran
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
- Department of Integrative Biology, University of Wisconsin - Madison, 250 N. Mills St.Madison, WI 53706, USA
| | - Robert A. Marick
- Department of Biochemistry, University of Wisconsin - Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Jacob M. Ogorek
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - John F. DeWild
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - David P. Krabbenhoft
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
- Department of Civil and Environmental Engineering, University of Wisconsin – Madison, 1415 Engineering Drive, Madison WI 53706, USA
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24
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Zayed A, El-Aasr M, Ibrahim ARS, Ulber R. Fucoidan Characterization: Determination of Purity and Physicochemical and Chemical Properties. Mar Drugs 2020; 18:E571. [PMID: 33228066 PMCID: PMC7699409 DOI: 10.3390/md18110571] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
Fucoidans are marine sulfated biopolysaccharides that have heterogenous and complicated chemical structures. Various sugar monomers, glycosidic linkages, molecular masses, branching sites, and sulfate ester pattern and content are involved within their backbones. Additionally, sources, downstream processes, and geographical and seasonal factors show potential effects on fucoidan structural characteristics. These characteristics are documented to be highly related to fucoidan potential activities. Therefore, numerous chemical qualitative and quantitative determinations and structural elucidation methods are conducted to characterize fucoidans regarding their physicochemical and chemical features. Characterization of fucoidan polymers is considered a bottleneck for further biological and industrial applications. Consequently, the obtained results may be related to different activities, which could be improved afterward by further functional modifications. The current article highlights the different spectrometric and nonspectrometric methods applied for the characterization of native fucoidans, including degree of purity, sugar monomeric composition, sulfation pattern and content, molecular mass, and glycosidic linkages.
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Affiliation(s)
- Ahmed Zayed
- Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany;
- Department of Pharmacognosy, Tanta University, College of Pharmacy, El-Guish Street, Tanta 31527, Egypt; (M.E.-A.); (A.-R.S.I.)
| | - Mona El-Aasr
- Department of Pharmacognosy, Tanta University, College of Pharmacy, El-Guish Street, Tanta 31527, Egypt; (M.E.-A.); (A.-R.S.I.)
| | - Abdel-Rahim S. Ibrahim
- Department of Pharmacognosy, Tanta University, College of Pharmacy, El-Guish Street, Tanta 31527, Egypt; (M.E.-A.); (A.-R.S.I.)
| | - Roland Ulber
- Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Gottlieb-Daimler-Straße 49, 67663 Kaiserslautern, Germany;
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25
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Capo E, Bravo AG, Soerensen AL, Bertilsson S, Pinhassi J, Feng C, Andersson AF, Buck M, Björn E. Deltaproteobacteria and Spirochaetes-Like Bacteria Are Abundant Putative Mercury Methylators in Oxygen-Deficient Water and Marine Particles in the Baltic Sea. Front Microbiol 2020; 11:574080. [PMID: 33072037 PMCID: PMC7536318 DOI: 10.3389/fmicb.2020.574080] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/25/2020] [Indexed: 11/13/2022] Open
Abstract
Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the composition and distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this knowledge gap, we used the Baltic Sea Reference Metagenome (BARM) dataset to study the abundance and distribution of the genes involved in Hg methylation (the hgcAB gene cluster). We determined the relative abundance of the hgcAB genes and their taxonomic identity in 81 brackish metagenomes that cover spatial, seasonal and redox variability in the Baltic Sea water column. The hgcAB genes were predominantly detected in anoxic water, but some hgcAB genes were also detected in hypoxic and normoxic waters. Phylogenetic analysis identified putative Hg methylators within Deltaproteobacteria, in oxygen-deficient water layers, but also Spirochaetes-like and Kiritimatiellaeota-like bacteria. Higher relative quantities of hgcAB genes were found in metagenomes from marine particles compared to free-living communities in anoxic water, suggesting that such particles are hotspot habitats for Hg methylators in oxygen-depleted seawater. Altogether, our work unveils the diversity of the microorganisms with the potential to mediate MeHg production in the Baltic Sea and pinpoint the important ecological niches for these microorganisms within the marine water column.
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Affiliation(s)
- Eric Capo
- Department of Chemistry, Umeå University, Umeå, Sweden.,Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andrea G Bravo
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Anne L Soerensen
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Caiyan Feng
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Anders F Andersson
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, Umeå, Sweden
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26
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Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz MF, Hehemann JH. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol 2020; 5:1026-1039. [PMID: 32451471 DOI: 10.1038/s41564-020-0720-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022]
Abstract
Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.
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Affiliation(s)
- Andreas Sichert
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Antonio Fernandez-Guerra
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany.
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27
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van Vliet DM, Lin Y, Bale NJ, Koenen M, Villanueva L, Stams AJM, Sánchez-Andrea I. Pontiella desulfatans gen. nov., sp. nov., and Pontiella sulfatireligans sp. nov., Two Marine Anaerobes of the Pontiellaceae fam. nov. Producing Sulfated Glycosaminoglycan-like Exopolymers. Microorganisms 2020; 8:microorganisms8060920. [PMID: 32570748 PMCID: PMC7356697 DOI: 10.3390/microorganisms8060920] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, we isolated two marine strains, F1T and F21T, which together with Kiritimatiella glycovorans L21-Fru-ABT are the only pure cultures of the class Kiritimatiellae within the phylum Verrucomicrobiota. Here, we present an in-depth genome-guided characterization of both isolates with emphasis on their exopolysaccharide synthesis. The strains only grew fermentatively on simple carbohydrates and sulfated polysaccharides. Strains F1T, F21T and K. glycovorans reduced elemental sulfur, ferric citrate and anthraquinone-2,6-disulfonate during anaerobic growth on sugars. Both strains produced exopolysaccharides during stationary phase, probably with intracellularly stored glycogen as energy and carbon source. Exopolysaccharides included N-sulfated polysaccharides probably containing hexosamines and thus resembling glycosaminoglycans. This implies that the isolates can both degrade and produce sulfated polysaccharides. Both strains encoded an unprecedently high number of glycoside hydrolase genes (422 and 388, respectively), including prevalent alpha-L-fucosidase genes, which may be necessary for degrading complex sulfated polysaccharides such as fucoidan. Strain F21T encoded three putative glycosaminoglycan sulfotransferases and a putative sulfate glycosaminoglycan biosynthesis gene cluster. Based on phylogenetic and chemotaxonomic analyses, we propose the taxa Pontiella desulfatans F1T gen. nov., sp. nov. and Pontiella sulfatireligans F21T sp. nov. as representatives of the Pontiellaceae fam. nov. within the class Kiritimatiellae.
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Affiliation(s)
- Daan M. van Vliet
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (D.M.v.V.); (A.J.M.S.)
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands;
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Landsdiep 4, 1797 SZ ’t Horntje (Texel), The Netherlands; (N.J.B.); (M.K.); (L.V.)
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Landsdiep 4, 1797 SZ ’t Horntje (Texel), The Netherlands; (N.J.B.); (M.K.); (L.V.)
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Landsdiep 4, 1797 SZ ’t Horntje (Texel), The Netherlands; (N.J.B.); (M.K.); (L.V.)
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (D.M.v.V.); (A.J.M.S.)
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (D.M.v.V.); (A.J.M.S.)
- Correspondence: ; Tel.: +31-317-483486
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28
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Ta DT, Lin CY, Ta TMN, Chu CY. Biohythane production via single-stage anaerobic fermentation using entrapped hydrogenic and methanogenic bacteria. BIORESOURCE TECHNOLOGY 2020; 300:122702. [PMID: 31918294 DOI: 10.1016/j.biortech.2019.122702] [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: 11/05/2019] [Revised: 12/24/2019] [Accepted: 12/26/2019] [Indexed: 06/10/2023]
Abstract
This study demonstrates the continuous biohythane production in a single-stage anaerobic digester using a biomass mixture of separately entrapped hydrogenic and methanogenic bacteria (H2- and CH4-producing bacteria, respectively). The entrapped hydrogenic/methanogenic bacteria biomass ratios of 1/4, 2/3, 3/2 and 4/1 were tested and shown to have a great effect on the single-stage biohythane production performance. At steady-states, the cultivations had biohythane production rates in the range of 381-480 mL/L-d, with H2 content in biohythane (HCH) varying from 1% to 75% (v/v) and chemical oxygen demand removal efficiencies (TCODre) of 57.6-81.9%. Biomass ratio 2/3 (weight ratio 1/1.5) resulted in peak biohythane production with H2 and CH4 production rates being 64.6 and 395 mL/L-d, respectively, HCH 15% and TCODre 74.4%. The novelty of this work is to show the potential of producing biohythane from an innovative single-stage dark fermentation system using entrapped hydrogenic and methanogenic bacteria.
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Affiliation(s)
- Doan Thanh Ta
- Department of Environmental Engineering and Science, Feng Chia University, Taiwan
| | - Chiu-Yue Lin
- Department of Environmental Engineering and Science, Feng Chia University, Taiwan; Green Energy and Biotechnology Industry Development Research Center, Feng Chia University, Taiwan.
| | - Thi Minh Ngoc Ta
- Faculty of Food Technology, Nhatrang University, Viet Nam; Food Technology Department, Ho Chi Minh City University of Technology, Viet Nam
| | - Chen-Yeon Chu
- Green Energy and Biotechnology Industry Development Research Center, Feng Chia University, Taiwan; Institute of Green Products, Feng Chia University, Taiwan
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29
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Edwards JE, Shetty SA, van den Berg P, Burden F, van Doorn DA, Pellikaan WF, Dijkstra J, Smidt H. Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species. Anim Microbiome 2020; 2:6. [PMID: 33499982 PMCID: PMC7807809 DOI: 10.1186/s42523-020-0023-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 01/29/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the world's domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fiber. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fiber degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity of the equine fecal microbiota to multiple species of equines. Core taxa shared by all the equine fecal samples (n = 70) were determined and an overview given of the microbiota across different equine types (horse, donkey, horse × donkey and zebra). RESULTS Equine type was associated with differences in both fecal microbial concentrations and community composition. Donkey was generally most distinct from the other equine types, with horse and zebra not differing. Despite this, a common bacterial core of eight OTUs (out of 2070) and 16 genus level groupings (out of 231) was found in all the fecal samples. This bacterial core represented a much larger proportion of the equine fecal microbiota than previously reported, primarily due to the detection of predominant core taxa belonging to the phyla Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaetes. The majority of the core bacterial taxa lack cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and predominant. CONCLUSIONS Whilst differences were observed between equine types, a core fecal microbiota existed across all the equines. This core was composed primarily of a few predominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the predominant taxa needs to be addressed, as their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem.
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Affiliation(s)
- J. E. Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE Netherlands
| | - S. A. Shetty
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE Netherlands
| | - P. van den Berg
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE Netherlands
| | - F. Burden
- The Donkey Sanctuary, Sidmouth, Devon EX10 ONU UK
| | - D. A. van Doorn
- Division of Nutrition, Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CM Netherlands
- Department of Equine Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL Netherlands
| | - W. F. Pellikaan
- Animal Nutrition Group, Wageningen University & Research, Wageningen, 6708 WD Netherlands
| | - J. Dijkstra
- Animal Nutrition Group, Wageningen University & Research, Wageningen, 6708 WD Netherlands
| | - H. Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708 WE Netherlands
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30
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Yuan Y, Che L, Qi C, Meng Z. Protective effects of polysaccharides on hepatic injury: A review. Int J Biol Macromol 2019; 141:822-830. [PMID: 31487518 DOI: 10.1016/j.ijbiomac.2019.09.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/26/2019] [Accepted: 09/01/2019] [Indexed: 12/12/2022]
Abstract
Chronic hepatic injury caused by hepatitis B and C virus (HBV and HCV) infection, high fat diet and alcohol intake has increased to be the critical promoter of hepatocellular carcinoma (HCC). These high risk factors set into motion a vicious cycle of hepatocyte death, inflammation and fibrosis that finally results in cirrhosis and HCC after several decades. However, the treatment options for HCC are very limited. Therefore, early treatment of liver injury may reduce the incidence and probability of HCC or delay the progression of HCC. Substantial ongoing research has focused on nontoxic biological macromolecules, mainly polysaccharides, which possess prominent efficacies on hepatoprotective activity. Based on these encouraging observations, a great deal of effort has been devoted to discovering novel polysaccharides for the development of effective therapeutics for hepatic injury. This review focuses on the protective effects of polysaccharides on liver injury, including hepatitis virus infection, nonalcoholic steatohepatitis, alcoholic liver disease and other hepatic injuries, and describes the underlying mechanisms.
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Affiliation(s)
- Ye Yuan
- Department of Medicine Laboratory, First Hospital, Jilin University, Changchun 130021, China
| | - Lihe Che
- Department of Infectious Disease, First Hospital, Jilin University, Changchun 130021, China
| | - Chong Qi
- Department of Translational Medicine Research Institute, First Hospital, Jilin University, Changchun, Jilin 130021, China
| | - Zhaoli Meng
- Department of Translational Medicine Research Institute, First Hospital, Jilin University, Changchun, Jilin 130021, China.
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