1
|
Zhao Q, Zhang M, Wu Z, Li Y, Jiang J, Qiu J. Dynamics of bacterial community in the foregut and hindgut of earthworms with the nutrition supplied by kitchen waste during vermicomposting. BIORESOURCE TECHNOLOGY 2023; 374:128777. [PMID: 36822551 DOI: 10.1016/j.biortech.2023.128777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/15/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Earthworm gut microbiota is vital in degrading bio-waste during vermicomposting. However, microbial dynamics in earthworm gut during this process are unclear. Thus, the aim is to firstly report the bacterial dynamics in both foregut and hindgut of earthworms over a 28 days' timeframe of vermicomposting by Eisenia foetida with the nutrition supplied by kitchen waste. Results showed that except the changing of the bacterial diversity, composition and structure, dynamics of the foregut and hindgut bacteria also differed during vermicomposting which related to the changes of nutrient provision. Day 3 was a turning point. The abundant bacteria of the top 20 % genera nearly did not overlap between the foregut and hindgut. In the end of vermicomposting, a remarkable stable bacterial structure appeared in the hindgut compared to somewhat muddled one in the foregut. Understanding the dynamics of earthworm gut microbiota enables the improvements to regulate the efficiency of organic waste vermicomposting.
Collapse
Affiliation(s)
- Qi Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Manrui Zhang
- Center of Wuxi Agricultural Product Quality Monitoring, Wuxi 214000, China
| | - Zexuan Wu
- Ecological Environment and Water Authority of Jiangbei New District, Nanjing 211899, China
| | - Yinsheng Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jibao Jiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiangping Qiu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
2
|
Song C, Zhou Y, Li X, Dong R, Song X, Huang Z, Dong D. Interaction among biofilter microbiome, fecal metabolome and water quality and regulation of sewage discharge in the recirculating aquaculture system of Apostichopus japonicus. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 330:117100. [PMID: 36608606 DOI: 10.1016/j.jenvman.2022.117100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
With the aggravation of environmental pollution caused by traditional culture of Apostichopus japonicus, the concept of A. japonicus recirculating aquaculture system (RAS) came into being. To plan the sewage discharge time reasonably, we explored the temporal variation of water quality, biofilter microbe and fecal metabolome in RAS and relevant mechanism. The results showed that monitored water quality in RAS were within the safe living range of A. japonicus. Proteobacteria and Desulfobacterota were dominant bacteria in biofilter. The RDA results and correlation heatmap showed that NH4-N and NO2-N significantly affected the microbial community composition. The expression pattern of fecal metabolites changed with the passage of time after feeding. And ROC curve analysis and VIP bar chart showed that there were inter group biomarkers with predictive performance, which could help to remind timely sewage discharge. Topological analysis of KEGG pathway enrichment showed that metabolic pathways such as alanine, aspartate and glutamate metabolism changed significantly after feeding (P < 0.01). Additionally, the correlation analysis results showed that biofilter microbe and fecal metabolites were related to water quality (P < 0.05). Combined with the above research results, this study concluded that the RAS could discharge sewage 25-30 h after feeding. These findings were of direct significance to the management of RAS environment and the protection of A. japonicus healthy growth.
Collapse
Affiliation(s)
- Chenyu Song
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Yijing Zhou
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Xian Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Ruiguang Dong
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Xiefa Song
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| | - Zhitao Huang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Dengpan Dong
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| |
Collapse
|
3
|
Deciphering waste bound nitrogen by employing psychrophillic Aporrectodea caliginosa and priming of coprolites by associated heterotrophic nitrifiers under high altitude Himalayas. Sci Rep 2022; 12:9556. [PMID: 35688921 PMCID: PMC9187671 DOI: 10.1038/s41598-022-12972-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Abstract
Himalayan ecosystem is characterized by its fragile climate with rich repositories of biodiversity. Waste collection and disposal are becoming increasingly difficult due to topographical variations. Aporrectodea caligenosa, a versatile psychrophillic soil dweller, is a useful biocatalyst with potent bio-augmented capability for waste treatment at low temperatures. Microcosm experiments were conducted to elucidate the comprehensive nature of biogenic nitrogen transformation to NH4+ and NO3− produced by coupling of earthworm-microbes. Higher biogenic recovery of NH4+-N from coprolites of garden soil (47.73 ± 1.16%) and Himalayan goat manure (86.32 ± 0.92%) with an increment of 14.12 and 47.21% respectively over their respective control (without earthworms) with a linear decline beyond 4th week of incubation was reported. NO3–-N recovery progressively sustained in garden soil and goat manure coprolites during entire incubation with highest 81.81 ± 0.45 and 87.20 ± 1.08 µg-N g−1dry weight recorded in 6th and 5th week of incubation respectively and peak increments as 38.58 and 53.71% relative to respective control (without earthworms). Declined NH4+–N in coprolites at low temperature (15.0 ± 2.0 °C) evidenced increased nitrification rates by taking over the process by abundant nitrifying microbes. Steady de-nitrification with progressive incubation on an average was 16.95 ± 0.46 ng-N g−1 per week and 21.08 ± 0.87 ng-N g−1 per week compared to 14.03 ± 0.58 ng-N g−1 per week and 4.50 ± 0.31 ng-N g−1 per week in respective control treatments. Simultaneous heterotrophic nitrification and aerobic denitrification (SHNAD) was found to be a prominent bioprocess at low temperature that resulted in high and stable total nitrogen and nitrate accumulation from garden soil and goat manure with relative recovery efficiency of 11.12%, 14.97% and 14.20%; 19.34%. A. caligenosa shows promising prospects for mass applicability in biogenic N removal from manure of Himalayan goat.
Collapse
|
4
|
Zhang Y, Yang Z, Li X, Song P, Wang J. Effects of diisononyl phthalate exposure on the oxidative stress and gut microorganisms in earthworms (Eisenia fetida). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153563. [PMID: 35104518 DOI: 10.1016/j.scitotenv.2022.153563] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/22/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Phthalate esters (PAEs) are widely used as plasticizers and can be ubiquitously detected in environment. However, the toxic effects and mechanisms of diisononyl phthalate (DINP) on earthworms are still poorly understood. In this study, earthworms (Eisenia fetida) were exposed to DINP at various doses (0, 300, 600, 1200, and 2400 mg/kg) to investigate their subchronic toxicity. The results demonstrated that the reactive oxygen species (ROS) levels displayed an "increase-decrease" trend with the increasing DINP doses after DINP exposure on days 7, 14, 21, and 28. The malondialdehyde (MDA) content increased with increasing DINP doses on days 7, 14, and then decreased on days 21, 28. The values of superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST) showed similar variation patterns and reached a maximum level on 21 d. Moreover, on day 28, the SOD and CAT gene expression levels were upregulated, while the GST gene expression levels were downregulated. Meanwhile, 16S rRNA genes of E. fetida gut bacteria and surrounding soil bacteria were measured after 28 days of exposure to DINP. The Chao index of E. fetida gut bacteria decreased when the treatment with the highest concentration (2400 mg/kg) was applied. At the phylum level, the abundance of Chloroflexi was significantly lower in the gut of E. fetida. In addition, the abundance of Proteobacteria at the phylum level and Ottowia at the genus level significantly increased in the surrounding soil. Overall, our results shed light on the toxic mechanism of DINP at biochemical, molecular, and omics levels, and contributed to a better understanding of the ecotoxicity of DINP.
Collapse
Affiliation(s)
- Youai Zhang
- College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
| | - Zhongkang Yang
- College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
| | - Xianxu Li
- College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
| | - Peipei Song
- College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
| | - Jun Wang
- College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China.
| |
Collapse
|
5
|
Metagenomic Exploration of Bacterial Community Structure of Earthworms’ Gut. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.3.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Living organisms are naturally bestowed with unique and imitable qualities for maintaining ecological balance and earthworms are no exceptions. These so-called keystone species of terrestrial ecosystems are equipped with wonderful machinery, allowing them to nurture soil beautifully. Earthworm gut represents a potential microbial reservoir, having a complex interdependence with the host. The study aimed to profile bacterial community structure of three earthworm species belonging to two different life forms; Perionyx excavatus and Eudrilus eugeniae (epigeic), Polypheretima elongata (endogeic) respectively. Diversity analysis using 16S amplicon sequencing revealed that the dominant phyla were Proteobacteria (34.17-77.88) followed by Actinobacteria (13.43-35.54%), Firmicutes (1.69-15.45%) and Bacteroidetes (0.51-8.12%). The alpha diversity indices explicit similar gut microbiota of Perionyx excavatus and Eudrilus eugeniae and while higher alpha diversity was recorded in comparison to Polypheretima elongata gut. The taxonomic to the phenotypic annotation of 16S rRNA metagenomes revealed that dominance of Gram-negative bacterial community in all earthworm species while, Polypheretima elongata comprises higher percentage (78%) of Gram-negative bacterial community to Perionyx excavatus (32.3%) and Eudrilus eugeniae (38.3%). The oxygen requirement phenotypic analysis showed that all earthworm species were abundant with aerobic followed by anaerobic bacterial groups. Furthermore, functional metabolism phenotypic analysis revealed that a high abundance of ammonia oxidizers (29.3-80.2%), the gut microbiomes showed the relative abundance of sulphate reducer (22.6-78.7%), nitrite reducer (19.8-73.2%), dehalogenators (12.6-25.1%), illustrating in the role of these microbial communities in various degradation and bioremediation processes. The present study signifies the intrinsic gut microbiota of earthworm species for intensified biodegradation.
Collapse
|
6
|
Bi QF, Jin BJ, Zhu D, Jiang YG, Zheng BX, O'Connor P, Yang XR, Richter A, Lin XY, Zhu YG. How can fertilization regimes and durations shape earthworm gut microbiota in a long-term field experiment? ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112643. [PMID: 34411817 DOI: 10.1016/j.ecoenv.2021.112643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
The positive roles of earthworms on soil functionality has been extensively documented. The capacity of the earthworm gut microbiota on decomposition and nutrient cycling under long-term fertilization in field conditions has rarely been studied. Here, we report the structural, taxonomic, and functional responses of Eisenia foetida and Pheretima guillelmi gut microbiota to different fertilization regimes and durations using 16S rRNA gene-based Illumina sequencing and high-throughput quantitative PCR techniques. Our results revealed that the core gut microbiota, especially the fermentative bacteria were mainly sourced from the soil, but strongly stimulated with species-specificity, potential benefits for the host and soil health. The functional compositions of gut microbiota were altered by fertilization with fertilization duration being more influential than fertilization regimes. Moreover, the combination of organic and inorganic fertilization with the longer duration resulted in a higher richness and connectivity in the gut microbiota, and also their functional potential related to carbon (C), nitrogen, and phosphorus cycling, particularly the labile C decomposition, denitrification, and phosphate mobilization. We also found that long-term inorganic fertilization increased the abundance of pathogenic bacteria in the P. guillelmi gut. This study demonstrates that understanding earthworm gut microbiota can provide insights into how agricultural practices can potentially alter soil ecosystem functions through the interactions between soil and earthworm gut microbiotas.
Collapse
Affiliation(s)
- Qing-Fang Bi
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bing-Jie Jin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yu-Gen Jiang
- Fuyang Agricultural Technology Popularization Center, Hangzhou 311400, PR China
| | - Bang-Xiao Zheng
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Lahti 15140, Finland
| | - Patrick O'Connor
- Centre for Global Food and Resources, University of Adelaide, Adelaide 5005, Australia
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China.
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| |
Collapse
|
7
|
Zhang L, Zhao T, Shi E, Zhang Z, Zhang Y, Chen Y. The non-negligibility of greenhouse gas emission from a combined pre-composting and vermicomposting system with maize stover and cow dung. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:19412-19423. [PMID: 33394443 DOI: 10.1007/s11356-020-12172-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
The acceptance of combined pre-composting and vermicomposting systems is increasing because of the advantage in rapidly stabilizing organic wastes and reducing emission of greenhouse gasses (GHG). However, GHG emission during the pre-composting phase is often neglected when evaluating the system. This study aimed to quantify GHG emission from a combined pre-composting and vermicomposting system and to investigate the effects of earthworms on GHG emission. A combined system using Eisenia fetida was employed to stabilize maize stover and cow dung (mixing ratio 60:40). The inoculating densities were 60 (T1), 120 (T2), and 180 (T3) earthworms per kilogram of substrate. A traditional composting system without earthworms was set as a control (T0). The results indicated that earthworms increased CO2 while decreased CH4 and N2O emissions compared to the control. Higher emission of CO2 suggested that the earthworms promoted the degradation of the substrates. Lower emission of CH4 and N2O showed the advantage of the combined system because CH4 and N2O possess extremely higher global warming potential than that of CO2. T2 is recommended for stabilizing maize stover and cow dung when making a tradeoff between stabilization rate and reduction of GHG. The percentages of GHG emission during pre-composting relative to total GHG emission in T1, T2, and T3 were 34%, 35%, and 30%, respectively. GHG emission is non-negligible when using a combined system, especially the emission of GHG during the pre-composting phase cannot be ignored.
Collapse
Affiliation(s)
- Lei Zhang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130022, China
| | - Tingting Zhao
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130022, China
| | - Enhui Shi
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130022, China
| | - Zunhao Zhang
- The Electron Microscopy Center, Jilin University, Changchun, 130000, China
| | - Yan Zhang
- Costal Research and Extension Center, Mississippi State University, Starkville, MS, 39567, USA
| | - Yuxiang Chen
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130022, China.
| |
Collapse
|
8
|
Sun M, Chao H, Zheng X, Deng S, Ye M, Hu F. Ecological role of earthworm intestinal bacteria in terrestrial environments: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140008. [PMID: 32562986 DOI: 10.1016/j.scitotenv.2020.140008] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 05/24/2020] [Accepted: 06/03/2020] [Indexed: 05/21/2023]
Abstract
Increasing evidence demonstrated the critical role the earthworm gut played in sustaining earthworm's metabolism and transformation of nutrients and pollutants in the environment. Being rich in nutrients, the earthworm gut is favorable for the colonization of (facultative) anaerobic bacteria, which bridge the host earthworm gut with adjacent terrestrial environment. Therefore, the status quo of earthworm gut research was primarily reviewed in this work. It was found that most studies focused on the bacterial composition and diversity of the earthworm gut, and their potential application in nutrient element and pollutant transformation, such as nitrification, methanogens, heavy metal detoxification, etc. Yet limited information was available about the specific mechanism of intestinal bacteria in nutrient and pollutant transformation. Therefore, in this work we highlighted the current problems and concluded the future prospect of worm's intestinal bacteria research. On one hand, high throughput sequencing and bioinformatics tools are critical to break the bottleneck in the intestinal bacteria research via clarifying the molecular mechanism involved in the transformation processes described above. In addition, a global dataset concerning worm gut bacteria will be needed to provide comprehensive information about intestinal bacteria pool, and act as a communication platform to further encourage the progress of worm gut research.
Collapse
Affiliation(s)
- Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Huizhen Chao
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoxuan Zheng
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaopo Deng
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
9
|
Zeibich L, Guhl J, Drake HL. Impact of water content and dietary organic carbon richness on gut bacteria in the earthworm Lumbricus terrestris. FEMS MICROBES 2020. [DOI: 10.1093/femsmc/xtaa002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
ABSTRACTMany higher and lower animal gut ecosystems have complex resident microbial communities. In contrast, ingested soil is the primary source of the gut microbial diversity of earthworms, invertebrates of fundamental importance to the terrestrial biosphere. Earthworms also harbor a few endemic bacteria including Tenericutes-affiliated Candidatus Lumbricincola of unknown function. Gut microbes are subject to nutrient fluctuations due to dilution effects during gut passage, the nutrient richness of the anoxic gut, and dietary organic carbon, factors that could alter their activity/detection. This study's objective was to assess the potential impact of these factors on the occurrence and activity of ingested and endemic bacteria in gut content of Lumbricus terrestris. Fermentation product profiles of anoxic undiluted and diluted gut content treatments were similar, suggesting that experimental increase in water content and nutrient dilution had marginal impact on fermentation. However, 16S ribosomal Ribonucleic Acid (16S rRNA) sequence abundances indicated that stimulated bacterial taxa were not identical in undiluted and diluted treatments, with dominate potentially functionally redundant phylotypes being affiliated to the Firmicutes, Fusobacteria and Proteobacteria. Although the earthworm-associated Tenericutes were not stimulated in these treatments, the occurrence of three Tenericutes-affiliated phylotypes varied with the organic carbon richness of the earthworm diet, with two phylotypes being associated with high organic carbon richness. 16S rRNA sequence abundances indicated that other dominant gut taxa also varied with dietary organic carbon richness. These findings illustrate that functionally redundant ingested bacteria and earthworm-associated Tenericutes might be influenced by nutrient fluctuations in the gut and organic carbon richness of the earthworm diet.
Collapse
Affiliation(s)
- Lydia Zeibich
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch Strasse 1-3, 95440 Bayreuth, Germany
| | - Jennifer Guhl
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch Strasse 1-3, 95440 Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch Strasse 1-3, 95440 Bayreuth, Germany
| |
Collapse
|
10
|
Liu P, Yang Y, Li M. Responses of soil and earthworm gut bacterial communities to heavy metal contamination. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114921. [PMID: 32540597 DOI: 10.1016/j.envpol.2020.114921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/21/2020] [Accepted: 05/30/2020] [Indexed: 05/24/2023]
Abstract
The large accumulation of heavy metals in the soil surrounding steel factories has become a severe environmental problem. However, few studies have focused on how the earthworm gut microbiota responds to heavy metals in the soil. This study used research sites at a steel factory in Nanjing, China, to investigate how the soil bacterial community and earthworm gut microbiota respond differently to heavy metal contamination using Illumina high-throughput sequencing targeting 16S rRNA genes. The bacterial community of earthworm guts showed a distinct structure compared with that of the soil, featuring a higher relative abundance of Proteobacteria (45.7%) and Bacteroidetes (18.8%). The bacterial community in the earthworm gut appeared more susceptible to heavy metal contamination compared with the soil community. For example, we identified 38 OTUs (Operational taxonomic units) significantly influenced by contamination among 186 abundant OTUs in the soil, whereas 63 out of the 127 abundant OTUs in the earthworm gut were altered significantly under contamination. This susceptibility may be partly explained by the lower alpha diversity and distinct microbial interactions in the gut. In addition, the accumulation of heavy metals also stimulated the growth of potential plant growth promoting bacteria (PGPB) in the earthworm gut, especially those related to indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) production, which may potentially benefit the phyto-remediation of heavy metals. These results contribute to our understanding of the soil biota and its interactions under heavy metal contamination and may provide further insights into the phyto-remediation of metal-contaminated soil.
Collapse
Affiliation(s)
- Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Yang Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China; Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mei Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China.
| |
Collapse
|
11
|
Wu J, Bai Y, Lu B, Zhao W, Forstner C, Menzies NW, Bertsch PM, Wang P, Kopittke PM. Silver Sulfide Nanoparticles Reduce Nitrous Oxide Emissions by Inhibiting Denitrification in the Earthworm Gut. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11146-11154. [PMID: 32790293 DOI: 10.1021/acs.est.0c01241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The accumulation of Ag2S in agricultural soil via application of Ag-containing sludge potentially affects the functioning of soil microorganisms and earthworms (EWs) due to the strong antimicrobial properties of Ag. This study examined the effects of Ag2S nanoparticles (Ag2S-NPs) on the EW-mediated (Eisenia fetida and Pontoscolex corethrurus) soil N cycle. We used 16S rRNA gene-based sequencing and quantitative polymerase chain reaction to examine the bacterial community and nitrification/denitrification-related gene abundance. The presence of either EWs or Ag significantly increased denitrification and N2O emissions. However, the addition of Ag2S to EW-inhabited soil reduced N2O emissions by 14-33%. Furthermore, Ag2S caused a low-dose stimulation but a high-dose inhibition to N2O flux from the EW gut itself. Accordingly, an increase in Ag in the EW gut caused a decrease in the relative abundance of denitrifiers in both the soil and the gut, especially for the dominant genus Bacillus. Ag2S also decreased the copy numbers of nitrification gene (nxrB) and denitrification genes (napA, nirS, and nosZ) in EW gut, leading to the observed decrease in N2O emissions. Collectively, applying Ag2S-containing sludge disturbs the denitrification function of the EW gut microbiota and the cycling of N in soil-based systems.
Collapse
Affiliation(s)
- Jingtao Wu
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Yunfei Bai
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Bingkun Lu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Zhao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Christian Forstner
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Neal W Menzies
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Paul M Bertsch
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia 4072, Queensland, Australia
- Land and Water Ecosciences Precinct, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park 4102, Queensland, Australia
| | - Peng Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia 4072, Queensland, Australia
| |
Collapse
|
12
|
Chao H, Sun M, Ye M, Zheng X, Hu F. World within world: Intestinal bacteria combining physiological parameters to investigate the response of Metaphire guillelmi to tetracycline stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114174. [PMID: 32066061 DOI: 10.1016/j.envpol.2020.114174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/30/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Due to the abusive usage of antibiotics in animal husbandry, a large amount of residual antibiotics has been released into the environment, therein posing great threat against both environment security and public health. Therefore, it is of great significance to investigate the toxicity of antibiotics on the widely-applied bioindicator-earthworm. In this work, the physiological parameters and the intestinal bacteria community of Metaphire guillelmi were monitored simultaneously to evaluate their sensitivity to the tetracycline (TC) exposure. As expected, the antioxidant enzyme activity and coelomocyte apoptosis acted fairly well as biomarkers for the TC toxicity. In contrast, the intestinal bacteria of Metaphire guillelmi responded varyingly to different TC doses. When TC concentration increased from 0 to 35.7 μg cm-2, the percentage of the Proteobacteria phylum declined significantly from 85.5% to 34.4%, while the proportions of the Firmicutes, Planctomycetes and Atinomycete phyla clearly increased (p < 0.05). Meanwhile, the levels of TC resistance genes tetA, tetC, and tetW increased with the increasing TC concentration, in contrast to the declined abundance in denitrifying genes nirS and nosZ (p < 0.05). By analyzing the correlation between the antioxidant enzyme activity and the dominant intestinal bacteria in the worm gut, it is interesting to found that the four dominant bacteria genera Mesorhizobium, Aliihoeflea, Romboutsia, and Nitrospira are the promising bioindicator of TC stress due to their sensitive response. This work shed novel light on evaluating the ecotoxicological risks posed by residual TC in environment by using a combination of physiological parameters and intestinal bacterial activity in earthworms.
Collapse
Affiliation(s)
- Huizhen Chao
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiaoxuan Zheng
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
13
|
Diversity and Metabolic Potential of Earthworm Gut Microbiota in Indo-Myanmar Biodiversity Hotspot. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.2.48] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
|
14
|
Zhou GW, Yang XR, Sun AQ, Li H, Lassen SB, Zheng BX, Zhu YG. Mobile Incubator for Iron(III) Reduction in the Gut of the Soil-Feeding Earthworm Pheretima guillelmi and Interaction with Denitrification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4215-4223. [PMID: 30882209 DOI: 10.1021/acs.est.8b06187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Diets of soil-feeding earthworms contain abundant nitrate and iron(III) oxides, which are potential electron acceptors for mineralization of organic compounds. The earthworm gut provides an ideal habitat for ingested iron(III)-reducing microorganisms. However, little is known about iron(III) reduction and its interaction with other processes in the guts of earthworms. Here, we determined the dynamics of iron(III) and revealed its interaction with the turnover of organic acids and nitrate in the gut of the earthworm Pheretima guillelmi. Samples from gut contents combined with anoxic incubation were used for chemical analysis and 16S rRNA based Illumina sequencing. Chemical analysis showed that higher ratios of iron(II)/iron(III), nitrite/nitrate, and more abundant organic acids were contained in the in vivo gut of the earthworm P. guillelmi than those in the in situ soil. A higher rate of iron(III) reduction was detected in treatments of microcosmic incubation with gut contents (IG gut) than that with soil (IG soil), and nitrate reduction occurred earlier than iron(III) reduction in both treatments. Potential iron(III) reducers were dominated by fermentative genera Clostridium, Bacillus, and Desulfotomaculum in the treatment of IG gut, while they were dominated by dissimilatory iron(III)-reducing genera Geobacter in the treatment of IG soil. The iron(III)-reducing microbial community shared several genera with denitrifers in the treatment of IG gut, revealing a close link between iron(III) reduction and denitrification in the gut of earthworms. Collectively, our findings demonstrated that iron(III) reduction occurred along the gut and provided novel insights into the great contribution of earthworm gut microbiota on Fe and the associated C and N cycling in soil environments.
Collapse
Affiliation(s)
- Guo-Wei Zhou
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
- State Key Lab of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , People's Republic of China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
| | - An-Qi Sun
- Department of Environmental Science and Engineering , Huaqiao University , Xiamen 361021 , People's Republic of China
| | - Hu Li
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
| | - Simon Bo Lassen
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
- Department of Plant and Environmental Sciences, Faculty of Science , University of Copenhagen , Thorvaldsensvej 40 , Frederiksberg 1871 , Denmark
| | - Bang-Xiao Zheng
- Falculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme , University of Helsinki , Niemenkatu 73 , Lahti 15140 , Finland
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
- State Key Lab of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , People's Republic of China
| |
Collapse
|
15
|
Liu B, Zhang X, Bakken LR, Snipen L, Frostegård Å. Rapid Succession of Actively Transcribing Denitrifier Populations in Agricultural Soil During an Anoxic Spell. Front Microbiol 2019; 9:3208. [PMID: 30671037 PMCID: PMC6331397 DOI: 10.3389/fmicb.2018.03208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/11/2018] [Indexed: 12/25/2022] Open
Abstract
Denitrification allows sustained respiratory metabolism during periods of anoxia, an advantage in soils with frequent anoxic spells. However, the gains may be more than evened out by the energy cost of producing the denitrification machinery, particularly if the anoxic spell is short. This dilemma could explain the evolution of different regulatory phenotypes observed in model strains, such as sequential expression of the four denitrification genes needed for a complete reduction of nitrate to N2, or a “bet hedging” strategy where all four genes are expressed only in a fraction of the cells. In complex environments such strategies would translate into progressive onset of transcription by the members of the denitrifying community. We exposed soil microcosms to anoxia, sampled for amplicon sequencing of napA/narG, nirK/nirS, and nosZ genes and transcripts after 1, 2 and 4 h, and monitored the kinetics of NO, N2O, and N2. The cDNA libraries revealed a succession of transcribed genes from active denitrifier populations, which probably reflects various regulatory phenotypes in combination with cross-talks via intermediates (NO2−, NO) produced by the “early onset” denitrifying populations. This suggests that the regulatory strategies observed in individual isolates are also displayed in complex communities, and pinpoint the importance for successive sampling when identifying active key player organisms.
Collapse
Affiliation(s)
- Binbin Liu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars Snipen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| |
Collapse
|
16
|
Zeibich L, Schmidt O, Drake HL. Fermenters in the earthworm gut: do transients matter? FEMS Microbiol Ecol 2018; 95:5185111. [DOI: 10.1093/femsec/fiy221] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/15/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lydia Zeibich
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| |
Collapse
|
17
|
Kiyasudeen K, Ibrahim MH, Muhammad SA, Ismail SA, Gonawan FN, Zuknik MH. Earthworms as plug flow reactors: a first-order kinetic study on the gut of the vermicomposting earthworm Eudrilus eugeniae. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:31062-31070. [PMID: 30187407 DOI: 10.1007/s11356-018-3074-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Earthworms are commonly referred as environmental engineers and their guts are often compared with chemical reactors. However, modeling experiments to substantiate it are lacking. The aim of this study was to use established reactor models, particularly PFR, on the gut of the vermicomposting earthworm Eudrilus eugeniae to understand more on its digestion. To achieve the objective, a mathematical model based on first-order kinetics was framed and used to determine the pattern of digestion rates of nutrient indicators, namely total carbon (%), total nitrogen (%), C/N ratio, 13C (‰), and 15N (‰) at five intersections (pre-intestine, foregut, midgut A, midgut B, and hindgut) along the gut of E. eugeniae. The experimental results revealed that the concentrations of TC, TN, 13C, and 15N decreased during gut transit, whereas C/N ratio increased. The first-order model demonstrated that all the nutrients exhibit a linear pattern of digestion during gut transit, which supports the PFR model. On this basis, the present study concludes that the gut of E. eugeniae functions as PFR.
Collapse
Affiliation(s)
- Katheem Kiyasudeen
- School of Industrial Technology, Environmental Technology Division, University Sains Malaysia, 11800 USM, Penang, Malaysia.
| | - Mahamad Hakimi Ibrahim
- School of Industrial Technology, Environmental Technology Division, University Sains Malaysia, 11800 USM, Penang, Malaysia
| | - Syahidah Akmal Muhammad
- School of Industrial Technology, Environmental Technology Division, University Sains Malaysia, 11800 USM, Penang, Malaysia
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
| | | | - Fadzil Noor Gonawan
- School of Chemical Engineering, Engineering Campus, Universiti Sains Malaysia, 14300, Nibong Tebal, Penang, Malaysia
| | - Mark Harris Zuknik
- School of Industrial Technology, Environmental Technology Division, University Sains Malaysia, 11800 USM, Penang, Malaysia
| |
Collapse
|
18
|
Fjøsne T, Myromslien FD, Wilson RC, Rudi K. Earthworms are associated with subpopulations of Gammaproteobacteria irrespective of the total soil microbiota composition and stability. FEMS Microbiol Lett 2018; 365:4951604. [PMID: 29579208 DOI: 10.1093/femsle/fny071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 03/21/2018] [Indexed: 02/01/2023] Open
Abstract
Soil represents one of the most complex microbial ecosystems on earth. It is well-known that invertebrates such as earthworms have a major impact on transformations of organic material in soil, while their effect on the soil microbiota remains largely unknown. The aim of our work was therefore to investigate the association of earthworms with temporal stability, composition and diversity in two soil microbiota experimental series. We found that earthworms were consistently associated with an increase in subgroups of Gammaproteobacteria, despite major differences in microbiota composition and temporal stability across the experimental series. Our results therefore suggest that earthworms can affect subpopulation dynamics in the soil microbiota, irrespective of the total microbiota composition. If the soil microbiota is comprised of independent microbiota components, this can contribute to our general understanding of the complexity of the soil microbiota.
Collapse
Affiliation(s)
- Trine Fjøsne
- Inland Norway University of Applied Sciences, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Department of Biotechnology, 2318 Hamar, Norway
| | - Frøydis D Myromslien
- Inland Norway University of Applied Sciences, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Department of Biotechnology, 2318 Hamar, Norway
| | - Robert C Wilson
- Inland Norway University of Applied Sciences, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Department of Biotechnology, 2318 Hamar, Norway
| | - Knut Rudi
- Inland Norway University of Applied Sciences, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Department of Biotechnology, 2318 Hamar, Norway.,Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| |
Collapse
|
19
|
Meier AB, Hunger S, Drake HL. Differential Engagement of Fermentative Taxa in Gut Contents of the Earthworm Lumbricus terrestris. Appl Environ Microbiol 2018; 84:e01851-17. [PMID: 29247057 PMCID: PMC5812936 DOI: 10.1128/aem.01851-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/08/2017] [Indexed: 11/20/2022] Open
Abstract
The earthworm gut is an anoxic, saccharide-rich microzone in aerated soils. The apparent degradation of diverse saccharides in the alimentary canal of the model earthworm Lumbricusterrestris is concomitant with the production of diverse organic acids, indicating that fermentation is an ongoing process in the earthworm gut. However, little is known about how different gut-associated saccharides are fermented. The hypothesis of this investigation was that different gut-associated saccharides differentially stimulate fermentative microorganisms in gut contents of L. terrestris This hypothesis was addressed by (i) assessing the fermentation profiles of anoxic gut content microcosms that were supplemented with gut-associated saccharides and (ii) the concomitant phylogenic analysis of 16S rRNA sequences. Galactose, glucose, maltose, mannose, arabinose, fucose, rhamnose, and xylose stimulated the production of fermentation products, including H2, CO2, acetate, lactate, propionate, formate, succinate, and ethanol. Fermentation profiles were dependent on the supplemental saccharide (e.g., glucose yielded large amounts of H2 and ethanol, whereas fucose did not, and maltose yielded large amounts of lactate, whereas mannose did not). Approximately 1,750,000 16S rRNA sequences were affiliated with 37 families, and phylogenic analyses indicated that a respective saccharide stimulated a subset of the diverse phylotypes. An Aeromonas-related phylotype displayed a high relative abundance in all treatments, whereas key Enterobacteriaceae-affiliated phylotypes were stimulated by some but not all saccharides. Collectively, these results reinforce the likelihood that (i) different saccharides stimulate different fermentations in gut contents of the earthworm and (ii) facultative aerobes related to Aeromonadaceae and Enterobacteriaceae can be important drivers of these fermentations.IMPORTANCE The feeding habits of earthworms influence the turnover of elements in the terrestrial biosphere. The alimentary tract of the earthworm constitutes an anoxic saccharide-rich microzone in aerated soils that offers ingested microbes a unique opportunity for anaerobic growth. The fermentative activity of microbes in the alimentary tract are responsible for the in situ production of (i) organic compounds that can be assimilated by the earthworm and (ii) H2 that is subject to in vivo emission by the earthworm and can be trophically linked to secondary microbial events in soils. To gain insight on how fermentative members of the gut microbiome might respond to the saccharide-rich alimentary canal, this study examines the impact of diverse gut-associated saccharides on the differential activation of fermentative microbes in gut contents of the model earthworm L. terrestris.
Collapse
Affiliation(s)
- Anja B Meier
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Sindy Hunger
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| |
Collapse
|
20
|
Braga LPP, Yoshiura CA, Borges CD, Horn MA, Brown GG, Drake HL, Tsai SM. Disentangling the influence of earthworms in sugarcane rhizosphere. Sci Rep 2016; 6:38923. [PMID: 27976685 PMCID: PMC5156904 DOI: 10.1038/srep38923] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/16/2016] [Indexed: 11/29/2022] Open
Abstract
For the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, we performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW−, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane. In EW+ treatments, N2O concentrations belowground (15 cm depth) and relative abundances of nitrous oxide genes (nosZ) were higher in bulk soil and rhizosphere, suggesting that soil microbes were able to consume earthworm-induced N2O. Shotgun sequencing (total DNA) revealed that around 70 microbial functions in bulk soil and rhizosphere differed between EW+ and EW− treatments. Overall, genes indicative of biosynthetic pathways and cell proliferation processes were enriched in EW+ treatments, suggesting a positive influence of worms. In EW+ rhizosphere, functions associated with plant-microbe symbiosis were enriched relative to EW− rhizosphere. Ecological networks inferred from the datasets revealed decreased niche diversification and increased keystone functions as an earthworm-derived effect. Plant biomass was improved in EW+ and worm population proliferated.
Collapse
Affiliation(s)
- Lucas P P Braga
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
| | - Clovis D Borges
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany.,Department of Ecological Microbiology, University of Bayreuth, Germany
| | | | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Germany
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
| |
Collapse
|
21
|
Chen C, Whalen JK. Earthworm interactions with denitrifying bacteria are scale-dependent: Evidence from physiological to riparian ecosystem scales. Basic Appl Ecol 2016. [DOI: 10.1016/j.baae.2015.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
22
|
Schulz K, Hunger S, Brown GG, Tsai SM, Cerri CC, Conrad R, Drake HL. Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil. THE ISME JOURNAL 2015; 9:1778-92. [PMID: 25615437 PMCID: PMC4511933 DOI: 10.1038/ismej.2014.262] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 11/28/2014] [Accepted: 12/05/2014] [Indexed: 11/09/2022]
Abstract
The anoxic saccharide-rich conditions of the earthworm gut provide an ideal transient habitat for ingested microbes capable of anaerobiosis. It was recently discovered that the earthworm Eudrilus eugeniae from Brazil can emit methane (CH4) and that ingested methanogens might be associated with this emission. The objective of this study was to resolve trophic interactions of bacteria and methanogens in the methanogenic food web in the gut contents of E. eugeniae. RNA-based stable isotope probing of bacterial 16S rRNA as well as mcrA and mrtA (the alpha subunit of methyl-CoM reductase and its isoenzyme, respectively) of methanogens was performed with [(13)C]-glucose as a model saccharide in the gut contents. Concomitant fermentations were augmented by the rapid consumption of glucose, yielding numerous products, including molecular hydrogen (H2), carbon dioxide (CO2), formate, acetate, ethanol, lactate, succinate and propionate. Aeromonadaceae-affiliated facultative aerobes, and obligate anaerobes affiliated to Lachnospiraceae, Veillonellaceae and Ruminococcaceae were associated with the diverse fermentations. Methanogenesis was ongoing during incubations, and (13)C-labeling of CH4 verified that supplemental [(13)C]-glucose derived carbon was dissimilated to CH4. Hydrogenotrophic methanogens affiliated with Methanobacteriaceae and Methanoregulaceae were linked to methanogenesis, and acetogens related to Peptostreptoccocaceae were likewise found to be participants in the methanogenic food web. H2 rather than acetate stimulated methanogenesis in the methanogenic gut content enrichments, and acetogens appeared to dissimilate supplemental H2 to acetate in methanogenic enrichments. These findings provide insight on the processes and associated taxa potentially linked to methanogenesis and the turnover of organic carbon in the alimentary canal of methane-emitting E. eugeniae.
Collapse
Affiliation(s)
- Kristin Schulz
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Sindy Hunger
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | | | - Siu M Tsai
- CENA-USP, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Carlos C Cerri
- CENA-USP, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| |
Collapse
|
23
|
Decleyre H, Heylen K, Sabbe K, Tytgat B, Deforce D, Van Nieuwerburgh F, Van Colen C, Willems A. A doubling of microphytobenthos biomass coincides with a tenfold increase in denitrifier and total bacterial abundances in intertidal sediments of a temperate estuary. PLoS One 2015; 10:e0126583. [PMID: 25961719 PMCID: PMC4427305 DOI: 10.1371/journal.pone.0126583] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/04/2015] [Indexed: 11/30/2022] Open
Abstract
Surface sediments are important systems for the removal of anthropogenically derived inorganic nitrogen in estuaries. They are often characterized by the presence of a microphytobenthos (MPB) biofilm, which can impact bacterial communities in underlying sediments for example by secretion of extracellular polymeric substances (EPS) and competition for nutrients (including nitrogen). Pyrosequencing and qPCR was performed on two intertidal surface sediments of the Westerschelde estuary characterized by a two-fold difference in MPB biomass but no difference in MPB composition. Doubling of MPB biomass was accompanied by a disproportionately (ten-fold) increase in total bacterial abundances while, unexpectedly, no difference in general community structure was observed, despite significantly lower bacterial richness and distinct community membership, mostly for non-abundant taxa. Denitrifier abundances corresponded likewise while community structure, both for nirS and nirK denitrifiers, remained unchanged, suggesting that competition with diatoms for nitrate is negligible at concentrations in the investigated sediments (appr. 1 mg/l NO3-). This study indicates that MPB biomass increase has a general, significantly positive effect on total bacterial and denitrifier abundances, with stimulation or inhibition of specific bacterial groups that however do not result in a re-structured community.
Collapse
Affiliation(s)
- Helen Decleyre
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- * E-mail:
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Bjorn Tytgat
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Carl Van Colen
- Marine Biology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
24
|
Murakami T, Segawa T, Bodington D, Dial R, Takeuchi N, Kohshima S, Hongoh Y. Census of bacterial microbiota associated with the glacier ice worm Mesenchytraeus solifugus. FEMS Microbiol Ecol 2015; 91:fiv003. [PMID: 25764456 DOI: 10.1093/femsec/fiv003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2014] [Indexed: 11/14/2022] Open
Abstract
The glacier ice worm, Mesenchytraeus solifugus, is a unique annelid, inhabiting only snow and ice in North American glaciers. Here, we analyzed the taxonomic composition of bacteria associated with M. solifugus based on the 16S rRNA gene. We analyzed four fixed-on-site and 10 starved ice worm individuals, along with glacier surface samples. In total, 1341 clones of 16S rRNA genes were analyzed for the ice worm samples, from which 65 bacterial phylotypes (99.0% cut-off) were identified. Of these, 35 phylotypes were closely related to sequences obtained from their habitat glacier and/or other components of cryosphere; whereas three dominant phylotypes were affiliated with animal-associated lineages of the class Mollicutes. Among the three, phylotype Ms-13 shared less than 89% similarity with database sequences and was closest to a gut symbiont of a terrestrial earthworm. Using fluorescence in situ hybridization, Ms-13 was located on the gut wall surface of the ice worms. We propose a novel genus and species, 'Candidatus Vermiplasma glacialis', for this bacterium. Our results raise the possibility that the ice worm has exploited indigenous glacier bacteria, while several symbiotic bacterial lineages have maintained their association with the ice worm during the course of adaptive evolution to the permanently cold environment.
Collapse
Affiliation(s)
- Takumi Murakami
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Takahiro Segawa
- National Institute of Polar Research, Tokyo 190-8518, Japan Transdisciplinary Research Integration Center, Tokyo 190-8518, Japan
| | - Dylan Bodington
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Roman Dial
- Department of Environmental Science, Alaska Pacific University, Alaska 99508, USA
| | - Nozomu Takeuchi
- Department of Earth Sciences, Chiba University, Chiba 263-8522, Japan
| | - Shiro Kohshima
- Wildlife Research Center, Kyoto University, Kyoto 606-8203, Japan
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| |
Collapse
|
25
|
Pass DA, Morgan AJ, Read DS, Field D, Weightman AJ, Kille P. The effect of anthropogenic arsenic contamination on the earthworm microbiome. Environ Microbiol 2014; 17:1884-96. [PMID: 25404571 DOI: 10.1111/1462-2920.12712] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/06/2014] [Accepted: 11/07/2014] [Indexed: 11/28/2022]
Abstract
Earthworms are globally distributed and perform essential roles for soil health and microbial structure. We have investigated the effect of an anthropogenic contamination gradient on the bacterial community of the keystone ecological species Lumbricus rubellus through utilizing 16S rRNA pyrosequencing for the first time to establish the microbiome of the host and surrounding soil. The earthworm-associated microbiome differs from the surrounding environment which appears to be a result of both filtering and stimulation likely linked to the altered environment associated with the gut micro-habitat (neutral pH, anoxia and increased carbon substrates). We identified a core earthworm community comprising Proteobacteria (∼50%) and Actinobacteria (∼30%), with lower abundances of Bacteroidetes (∼6%) and Acidobacteria (∼3%). In addition to the known earthworm symbiont (Verminephrobacter sp.), we identified a potential host-associated Gammaproteobacteria species (Serratia sp.) that was absent from soil yet observed in most earthworms. Although a distinct bacterial community defines these earthworms, clear family- and species-level modification were observed along an arsenic and iron contamination gradient. Several taxa observed in uncontaminated control microbiomes are suppressed by metal/metalloid field exposure, including eradication of the hereto ubiquitously associated Verminephrobacter symbiont, which raises implications to its functional role in the earthworm microbiome.
Collapse
Affiliation(s)
- Daniel Antony Pass
- Cardiff School of Biosciences, BIOSI 1, University of Cardiff, P.O. Box 915, Cardiff, Wales, CF10 3TL, UK
| | - Andrew John Morgan
- Cardiff School of Biosciences, BIOSI 1, University of Cardiff, P.O. Box 915, Cardiff, Wales, CF10 3TL, UK
| | - Daniel S Read
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Dawn Field
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Andrew J Weightman
- Cardiff School of Biosciences, BIOSI 1, University of Cardiff, P.O. Box 915, Cardiff, Wales, CF10 3TL, UK
| | - Peter Kille
- Cardiff School of Biosciences, BIOSI 1, University of Cardiff, P.O. Box 915, Cardiff, Wales, CF10 3TL, UK
| |
Collapse
|