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Dar MA, Xie R, Jing L, Qing X, Ali S, Pandit RS, Shaha CM, Sun J. Elucidating the structure, and composition of bacterial symbionts in the gut regions of wood-feeding termite, Coptotermes formosanus and their functional profile towards lignocellulolytic systems. Front Microbiol 2024; 15:1395568. [PMID: 38846576 PMCID: PMC11155305 DOI: 10.3389/fmicb.2024.1395568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/22/2024] [Indexed: 06/09/2024] Open
Abstract
The wood-feeding termite, Coptotermes formosanus, presents an efficient lignocellulolytic system, offering a distinctive model for the exploration of host-microbial symbiosis towards lignocellulose degradation. Despite decades of investigation, understanding the diversity, community structure, and functional profiles of bacterial symbionts within specific gut regions, particularly the foregut and midgut of C. formosanus, remains largely elusive. In light of this knowledge gap, our efforts focused on elucidating the diversity, community composition and functions of symbiotic bacteria inhabiting the foregut, midgut, and hindgut of C. formosanus via metagenomics. The termite harbored a diverse community of bacterial symbionts encompassing 352 genera and 26 known phyla, exhibiting an uneven distribution across gut regions. Notably, the hindgut displayed a higher relative abundance of phyla such as Bacteroidetes (56.9%) and Spirochetes (23.3%). In contrast, the foregut and midgut were predominantly occupied by Proteobacteria (28.9%) and Firmicutes (21.2%) after Bacteroidetes. The foregut harbored unique phyla like Candidate phylum_TM6 and Armatimonadetes. At the family level, Porphyromonadaceae (28.1, 40.6, and 53.5% abundance in foregut, midgut, and hindgut, respectively) and Spirochaetaceae (foregut = 9%, midgut = 16%, hindgut = 21.6%) emerged as dominant families in the termite's gut regions. Enriched operational taxonomic units (OTUs) were most abundant in the foregut (28), followed by the hindgut (14), while the midgut exhibited enrichment of only two OTUs. Furthermore, the functional analyses revealed distinct influences of bacterial symbionts on various metabolic pathways, particularly carbohydrate and energy metabolisms of the host. Overall, these results underscore significant variations in the structure of the bacterial community among different gut regions of C. formosanus, suggesting unique functional roles of specific bacteria, thereby inspiring further investigations to resolve the crosstalk between host and microbiomes in individual gut-regions of the termite.
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Affiliation(s)
- Mudasir A. Dar
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Rongrong Xie
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
| | - Luohui Jing
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
| | - Xu Qing
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
| | - Shehbaz Ali
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
| | | | - Chaitali M. Shaha
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
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Xu Y, Wang Y, Zheng A, Yuan Y, Xu L, Tang Y, Qin Q. Efficient biostimulation of microbial dechlorination of polychlorinated biphenyls by acetate and lactate under nitrate reducing conditions: Insights into dechlorination pathways and functional genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133775. [PMID: 38367444 DOI: 10.1016/j.jhazmat.2024.133775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 02/19/2024]
Abstract
Microbial-catalyzed reductive dechlorination of polychlorinated biphenyls (PCBs) is largely affected by the indigenous sediment geochemical properties. In this study, the effects of nitrate on PCB dechlorination and microbial community structures were first investigated in Taihu Lake sediment microcosms. And biostimulation study was attempted supplementing acetate/lactate. PCB dechlorination was apparently inhibited under nitrate-reducing conditions. Lower PCB dechlorination rate and less PCB dechlorination extent were observed in nitrate amended sediment microcosms (T-N) than those in non-nitrate amended microcosms (T-1) during 66 weeks of incubation. The total PCB mass reduction in T-N was 17.6% lower than that in T-1. The flanked-para dechlorination was completely inhibited, while the ortho-flanked meta dechlorination was only partially inhibited in T-N. The 7.5 mM of acetate/lactate supplementation recovered PCB dechlorination by resuming ortho-flanked meta dechlorination. Repeated additions of lactate showed more effective biostimulation than acetate. Phylum Chloroflexi, containing most known PCB dechlorinators, was found to play a vital role on stability of the network structures. In T-N, putative dechlorinating Chloroflexi, Dehalococcoides and RDase genes rdh12, pcbA4, pcbA5 all declined. With acetate/lactate supplementation, Dehalococcoides grew by 1-2 orders of magnitude and rdh12, pcbA4, pcbA5 increased by 1-3 orders of magnitude. At Week 66, parent PCBs declined by 86.4% and 80.9% respectively in T-N-LA and T-N-AC compared to 69.9% in T-N. These findings provide insights into acetate/lactate biostimulation as a cost-effective approach for treating PCB contaminated sediments undergoing nitrate inhibition.
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Affiliation(s)
- Yan Xu
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Ying Wang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - An Zheng
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yaping Yuan
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Lei Xu
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yanqiang Tang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Qingdong Qin
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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Alom MS, Cen Y, Tang R, Chen D, Dou H, Mo Z, Du H. Change of termite hindgut metabolome and bacteria after captivity indicates the hindgut microbiota provides nutritional factors to the host. Front Bioeng Biotechnol 2024; 11:1228918. [PMID: 38288244 PMCID: PMC10823432 DOI: 10.3389/fbioe.2023.1228918] [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: 06/07/2023] [Accepted: 12/01/2023] [Indexed: 01/31/2024] Open
Abstract
The gut-dwelling microbiota is an indispensable part of termites. It is influenced by a series of factors, such as diet and captivity. The objectives of this study were to study the metabolic functions of hindgut microbiota and to investigate the influence of captivity on the hindgut microbiota. The dampwood termite Hodotermopsis sjostedti was reared in the laboratory for 6 months. We conducted the metabolome analysis of the fat body from the freshly-collected workers (FBF), the hindgut fluid of the freshly-collected workers (HFF), and the hindgut fluid of laboratory-maintained workers. In addition, the 16S rRNA genes from the hindgut bacteria in the freshly-collected and laboratory-maintained workers were sequenced. According to our results, the concentrations of metabolites associated with amino acid biosynthesis, vitamin biosynthesis, fatty acid biosynthesis, and cofactor biosynthesis were higher in HFF compared with those in FBF, suggesting that the hindgut microbiota provides nutritional factors to the host. However, after captivity, the concentrations of metabolites in the hindgut associated with amino acid biosynthesis, nucleotide sugar metabolism, vitamin biosynthesis, and carbon metabolism decreased, while those associated with the steroid hormone biosynthesis and ovarian steroidogenesis increased. Meanwhile, the 16S amplicon study revealed that the abundance of certain bacteria changed after captivity, such as uncultured Termite Group 1 bacterium, Candidatus Symbiothrix dinenymphae, and unclassified Desulfovibrio. Our findings show that captivity influences the hindgut microbiota and shed light on the metabolic potential of the hindgut microbiota.
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Affiliation(s)
- Most Shormi Alom
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yijing Cen
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Rui Tang
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Dasong Chen
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Hongliang Dou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Zhenzuan Mo
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - He Du
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
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Wang S, Su M, Hu X, Wang X, Han Q, Yu Q, Heděnec P, Li H. Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny. FEMS Microbiol Lett 2024; 371:fnad135. [PMID: 38124623 DOI: 10.1093/femsle/fnad135] [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: 08/30/2023] [Revised: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.
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Affiliation(s)
- Sijie Wang
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
| | - Ming Su
- Central South Inventory and Planning Institute of National Forestry and Grassland Administration, 143 Xiangzhang East Road, Changsha, Hunan Province 410014, China
| | - Xueqian Hu
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, 768 Jiayuguan West Road, Lanzhou, Gansu Province 730020, China
| | - Petr Heděnec
- Institute for Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Huan Li
- School of Public Health, Lanzhou University, 199 Donggang West Road, Lanzhou, Gansu Province 730000, China
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, 768 Jiayuguan West Road, Lanzhou, Gansu Province 730020, China
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Junrui-Fu, Rong Z, Huang X, Wang J, Long X, Feng Q, Deng H. Gut dysbacteriosis induces expression differences in the adult head transcriptome of Spodoptera frugiperda in a sex-specific manner. BMC Microbiol 2023; 23:388. [PMID: 38057708 DOI: 10.1186/s12866-023-03089-0] [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: 08/15/2023] [Accepted: 10/25/2023] [Indexed: 12/08/2023] Open
Abstract
Mounting evidence indicates that the gut microbiota influences the neurodevelopment and behavior of insects through the gut-brain axis. However, it is currently unclear whether the gut microbiota affect the head profiles and immune pathway in pests. Here, we find that gut bacteria is essential for the immune and neural development of adult Spodoptera frugiperda, which is an extremely destructive agricultural pest worldwide. 16 S rRNA sequencing analysis showed that antibiotics exposure significantly disturbed the composition and diversity of gut bacteria. Further transcriptomic analysis revealed that the adult head transcripts were greatly affected by gut dysbacteriosis, and differently expression genes critical for brain and neural development including A4galt, Tret1, nsun4, Galt, Mitofilin, SLC2A3, snk, GABRB3, Oamb and SLC6A1 were substantially repressed. Interestingly, the dysbacteriosis caused sex-specific differences in immune response. The mRNA levels of pll (serine/threonine protein kinase Pelle), PGRP (peptidoglycan-sensing receptor), CECA (cecropin A) and CECB (cecropin B) involved in Toll and Imd signaling pathway were drastically decreased in treated male adults' heads but not in female adults; however, genes of HIVEP2, ZNF131, inducible zinc finger protein 1-like and zinc finger protein 99-like encoding zinc-finger antiviral protein (ZAP) involved in the interferon (IFNα/β) pathway were significantly inhibited in treated female adults' heads. Collectively, these results demonstrate that gut microbiota may regulate head transcription and impact the S. frugiperda adults' heads through the immune pathway in a sex-specific manner. Our finding highlights the relationship between the gut microbiota and head immune systems of S. frugiperda adults, which is an astonishing similarity with the discoveries of other animals. Therefore, this is the basis for further research to understand the interactions between hosts and microorganisms via the gut-brain axis in S. frugiperda and other insects.
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Affiliation(s)
- Junrui-Fu
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zixia Rong
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Ximei Huang
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Junhan Wang
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xiaoyan Long
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Qili Feng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Huimin Deng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510631, China.
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou, 514779, China.
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Chen J, Setia G, Lin LH, Sun Q, Husseneder C. Weight and protozoa number but not bacteria diversity are associated with successful pair formation of dealates in the Formosan subterranean termite, Coptotermes formosanus. PLoS One 2023; 18:e0293813. [PMID: 37956140 PMCID: PMC10642788 DOI: 10.1371/journal.pone.0293813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
New colonies of Formosan subterranean termites are founded by monogamous pairs. During swarming season, alates (winged reproductives) leave their parental colony. After swarming, they drop to the ground, shed their wings, and male and female dealates find suitable nesting sites where they mate and become kings and queens of new colonies. The first generation of offspring is entirely dependent on the nutritional resources of the founder pair consisting of the fat and protein reserves of the dealates and their microbiota, which include the cellulose-digesting protozoa and diverse bacteria. Since termite kings and queens can live for decades, mate for life and colony success is linked to those initial resources, we hypothesized that gut microbiota of founders affect pair formation. To test this hypothesis, we collected pairs found in nest chambers and single male and female dealates from four swarm populations. The association of three factors (pairing status, sex of the dealates and population) with dealate weights, total protozoa, and protozoa Pseudotrichonympha grassii numbers in dealate hindguts was determined. In addition, Illumina 16S rRNA gene sequencing and the QIIME2 pipeline were used to determine the impact of those three factors on gut bacteria diversity of dealates. Here we report that pairing status was significantly affected by weight and total protozoa numbers, but not by P. grassii numbers and bacteria diversity. Weight and total protozoa numbers were higher in paired compared to single dealates. Males contained significantly higher P. grassii numbers and bacteria richness and marginally higher phylogenetic diversity despite having lower weights than females. In conclusion, this study showed that dealates with high body weight and protozoa numbers are more likely to pair and become colony founders, probably because of competitive advantage. The combined nutritional resources provided by body weight and protozoa symbionts of the parents are important for successful colony foundation and development.
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Affiliation(s)
- Junyan Chen
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, Los Angeles, United States of America
| | - Garima Setia
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, Los Angeles, United States of America
| | - Li-Hsiang Lin
- Department of Experimental Statistics, Louisiana State University Agricultural Center, Baton Rouge, Los Angeles, United States of America
| | - Qian Sun
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, Los Angeles, United States of America
| | - Claudia Husseneder
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, Los Angeles, United States of America
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Cleary DFR, de Voogd NJ, Stuij TM, Swierts T, Oliveira V, Polónia ARM, Louvado A, Gomes NCM, Coelho FJRC. A Study of Sponge Symbionts from Different Light Habitats. MICROBIAL ECOLOGY 2023; 86:2819-2837. [PMID: 37597041 PMCID: PMC10640470 DOI: 10.1007/s00248-023-02267-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023]
Abstract
The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.
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Affiliation(s)
- D F R Cleary
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands.
| | - T M Stuij
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - T Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - V Oliveira
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Polónia
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A Louvado
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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Do TH, Dao TK, Nguyen HD, Truong NH. Understanding the Role of Free-Living Bacteria in the Gut of the Lower Termite Coptotermes gestroi Based on Metagenomic DNA Analysis. INSECTS 2023; 14:832. [PMID: 37999031 PMCID: PMC10671698 DOI: 10.3390/insects14110832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/28/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
Abstract
Termites' digestive systems, particularly in lower termites with the presence of protozoa, are unique ecological niches that shelter a diverse microbiota with a variety of functions for the host and the environment. In 2012, the metagenomic DNA (5.4 Gb) of the prokaryotes that freely live in the gut of the lower termite Coptotermes gestroi were sequenced. A total of 125,431 genes were predicted and analyzed in order to mine lignocellulolytic genes. however, the overall picture of the structure, diversity, and function of the prokaryotic gut microbiota was not investigated. In the present study, these 125,431 genes were taxonomically classified by MEGAN and functionally annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and by the Carbohydrate-Active enZYmes (CAZy) and HMMER databases. As a result, 95,751 bacterial genes were classified into 35 phyla. The structure of the bacteria, typified by a high ratio of Firmicutes to Bacterioidetes, was distinct from the structure of the entirety of the bacteria in the lower or higher termites' guts. The archaea (533 genes) were distributed into 4 phyla, 10 classes, 15 orders, 21 families, 47 genera, and 61 species. Although freely living in the guts, the prokaryotic community was formed, developed, and adapted to exhibit unique interactions in order to perform mutual roles of benefit to their hosts. Methanobacteriales, accounting for 61% of the archaea symbionts, seem to play an important role in methanogenesis. Concomitantly, bacterial methanotrophs in the gut utilize methane and combine with other bacterial groups, including potential lignocellulolytic degraders, acetogens, sulfur bacteria, and nitrogen-recycling bacteria, to efficiently convert wood with little nitrogen into acetates via certain pathway modules specified by prokaryotes that freely live in the gut. This forms an important energy source for the termites. Furthermore, bacteria carry 2223 genes involved in the biosynthesis of 17 antibiotic groups. The gut bacteria also possess genes for the degradation of 18 toxic aromatic compounds, of which four are commercial pesticides against termites commonly used for the preservation of wooden constructions. Eight of the eighteen pathways were the first to be reported from the termite gut. Overall, this study sheds light on the roles of the freely living bacteria and archaea in the C. gestroi gut, providing evidence that the gut microbiome acts as the second host genome, contributing both nutrients and immunity to support the host's existence, growth, and development.
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Affiliation(s)
- Thi Huyen Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam; (T.K.D.); (H.D.N.); (N.H.T.)
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam
| | - Trong Khoa Dao
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam; (T.K.D.); (H.D.N.); (N.H.T.)
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam
| | - Hong Duong Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam; (T.K.D.); (H.D.N.); (N.H.T.)
| | - Nam Hai Truong
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam; (T.K.D.); (H.D.N.); (N.H.T.)
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Cau Giay, Ha Noi 10000, Vietnam
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Garg A, Gadi VK, Zhu HH, Sarmah AK, Sreeja P, Sekharan S. A geotechnical perspective on soil-termite interaction: Role of termites in unsaturated soil properties. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:164864. [PMID: 37331385 DOI: 10.1016/j.scitotenv.2023.164864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/24/2023] [Accepted: 06/11/2023] [Indexed: 06/20/2023]
Abstract
The soil-insect interaction has gathered significant attention in the recent years due to its contribution to bio-cementation. Termites, as a group of cellulose-eating insects, alter physical (texture) and chemical (chemical composition) properties of soil. Conversely, physico-chemical properties of soil also influence termite activities. It is vital to understand the soil-termite interaction and their influence on hydraulic properties and shear strength of soil, which are related to a series of geotechnical engineering problems such as ground water recharge, runoff, erosion and stability of slopes. In this study, an attempt has been made to review the latest developments and research gaps in our understanding of soil-termite interaction within the context of geo-environmental engineering. The hydraulic properties and shear strength of termite modified soil were discussed with respect to soil texture, density and physico-chemical composition. The incorporation of hysteresis effect of soil water characteristic curve, and spatio-temporal variations of hydraulic conductivity and shear strength of termite modified soil is proposed to be considered in geotechnical engineering design and construction. Finally, the challenges and future trends in this research area are presented. The expertise from both geotechnical engineering and entomology is needed to plan future research with an aim to promote use of termites as maintenance engineers in geotechnical infrastructure.
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Affiliation(s)
- Ankit Garg
- Department of Civil and Environmental Engineering, Shantou University, China.
| | - Vinay Kumar Gadi
- Department of Civil and Environmental Engineering, Cardiff University, United Kingdom.
| | - Hong-Hu Zhu
- School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China.
| | - Ajit K Sarmah
- Department of Civil & Environmental Engineering, The Faculty of Engineering, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - P Sreeja
- Department of Civil Engineering, Indian Institute of Technology Guwahati, India.
| | - Sreedeep Sekharan
- Department of Civil Engineering, Indian Institute of Technology Guwahati, India.
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10
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Fu J, Wang J, Huang X, Guan B, Feng Q, Deng H. Composition and diversity of gut microbiota across developmental stages of Spodoptera frugiperda and its effect on the reproduction. Front Microbiol 2023; 14:1237684. [PMID: 37789854 PMCID: PMC10543693 DOI: 10.3389/fmicb.2023.1237684] [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: 06/09/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction Spodoptera frugiperda is a serious world-wide agricultural pest. Gut microorganisms play crucial roles in growth, development, immunity and behavior of host insects. Methods Here, we reported the composition of gut microbiota in a laboratory-reared strain of S. frugiperda using 16S rDNA sequencing and the effects of gut microbiota on the reproduction. Results Proteobacteria and Firmicutes were the predominant bacteria and the taxonomic composition varied during the life cycle. Alpha diversity indices indicated that the eggs had higher bacterial diversity than larvae, pupae and adults. Furthermore, eggs harbored a higher abundance of Ralstonia, Sediminibacterium and microbes of unclassified taxonomy. The dynamics changes in bacterial communities resulted in differences in the metabolic functions of the gut microbiota during development. Interestingly, the laid eggs in antibiotic treatment groups did not hatch much due to the gut dysbacteriosis, the results showed gut microbiota had a significant impact on the male reproduction. Discussion Our findings provide new perspectives to understand the intricate associations between microbiota and host, and have value for the development of S. frugiperda management strategies focusing on the pest gut microbiota.
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Affiliation(s)
- Junrui Fu
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junhan Wang
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ximei Huang
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Boyang Guan
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qili Feng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
| | - Huimin Deng
- Guangdong Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology and School of Life Sciences, South China Normal University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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11
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Diner RE, Zimmer-Faust A, Cooksey E, Allard S, Kodera SM, Kunselman E, Garodia Y, Verhougstraete MP, Allen AE, Griffith J, Gilbert JA. Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters. Appl Environ Microbiol 2023; 89:e0031823. [PMID: 37318344 PMCID: PMC10370324 DOI: 10.1128/aem.00318-23] [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: 02/28/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023] Open
Abstract
Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter-feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to the microbial ecology of pathogenic bacteria and their relationship with oyster hosts likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of Vibrio parahaemolyticus, Vibrio vulnificus, or fecal indicator bacteria. Site-specific environmental conditions significantly influenced microbial communities and potential pathogen concentrations in water. Oyster microbial communities, however, exhibited less variability in microbial community diversity and accumulation of target bacteria overall and were less impacted by environmental differences between sites. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated levels of potential pathogens. For example, increased levels of V. parahaemolyticus were associated with higher relative abundances of cyanobacteria, which could represent an environmental vector for Vibrio spp. transport, and with decreased relative abundance of Mycoplasma and other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters. IMPORTANCE Bacteria in the marine environment cause thousands of human illnesses annually. Bivalves are a popular seafood source and are important in coastal ecology, but their ability to concentrate pathogens from the water can cause human illness, threatening seafood safety and security. To predict and prevent disease, it is critical to understand what causes pathogenic bacteria to accumulate in bivalves. In this study, we examined how environmental factors and host and water microbial communities were linked to potential human pathogen accumulation in oysters. Oyster microbial communities were more stable than water communities, and both contained the highest concentrations of Vibrio parahaemolyticus at sites with warmer temperatures and lower salinities. High oyster V. parahaemolyticus concentrations corresponded with abundant cyanobacteria, a potential vector for transmission, and a decrease in potentially beneficial oyster microbes. Our study suggests that poorly understood factors, including host and water microbiota, likely play a role in pathogen distribution and pathogen transmission.
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Affiliation(s)
- Rachel E. Diner
- University of California, San Diego, Department of Pediatrics, La Jolla, California, USA
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Amy Zimmer-Faust
- Southern California Coastal Water Research Project, Microbiology Group, Costa Mesa, California, USA
| | - Emily Cooksey
- Environment, Exposure Science and Risk Assessment Center, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, Arizona, USA
| | - Sarah Allard
- University of California, San Diego, Department of Pediatrics, La Jolla, California, USA
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Sho M. Kodera
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Emily Kunselman
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Yash Garodia
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Marc P. Verhougstraete
- Environment, Exposure Science and Risk Assessment Center, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, Arizona, USA
| | - Andrew E. Allen
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
- J. Craig Venter Institute, Environmental and Microbial Genomics Group, La Jolla, California, USA
| | - John Griffith
- Southern California Coastal Water Research Project, Microbiology Group, Costa Mesa, California, USA
| | - Jack A. Gilbert
- University of California, San Diego, Department of Pediatrics, La Jolla, California, USA
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
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12
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Monti M, Giorgi A, Kemp DW, Olson JB. Spatial, temporal and network analyses provide insights into the dynamics of the bacterial communities associated with two species of Caribbean octocorals and indicate possible key taxa. Symbiosis 2023; 90:1-14. [PMID: 37360551 PMCID: PMC10238251 DOI: 10.1007/s13199-023-00923-x] [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: 11/03/2022] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
Abstract
Despite the current decline of scleractinian coral populations, octocorals are thriving on reefs in the Caribbean Sea and western North Atlantic Ocean. These cnidarians are holobiont entities, interacting with a diverse array of microorganisms. Few studies have investigated the spatial and temporal stability of the bacterial communities associated with octocoral species and information regarding the co-occurrence and potential interactions between specific members of these bacterial communities remain sparse. To address this knowledge gap, this study investigated the stability of the bacterial assemblages associated with two common Caribbean octocoral species, Eunicea flexuosa and Antillogorgia americana, across time and geographical locations and performed network analyses to investigate potential bacterial interactions. Results demonstrated that general inferences regarding the spatial and temporal stability of octocoral-associated bacterial communities should not be made, as host-specific characteristics may influence these factors. In addition, network analyses revealed differences in the complexity of the interactions between bacteria among the octocoral species analyzed, while highlighting the presence of genera known to produce bioactive secondary metabolites in both octocorals that may play fundamental roles in structuring the octocoral-associated bacteriome. Supplementary Information The online version contains supplementary material available at 10.1007/s13199-023-00923-x.
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Affiliation(s)
- M. Monti
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - A. Giorgi
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - D. W. Kemp
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - J. B. Olson
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
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Chakraborty A, Šobotník J, Votýpková K, Hradecký J, Stiblik P, Synek J, Bourguignon T, Baldrian P, Engel MS, Novotný V, Odriozola I, Větrovský T. Impact of Wood Age on Termite Microbial Assemblages. Appl Environ Microbiol 2023; 89:e0036123. [PMID: 37067424 PMCID: PMC10231148 DOI: 10.1128/aem.00361-23] [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: 03/03/2023] [Accepted: 03/25/2023] [Indexed: 04/18/2023] Open
Abstract
The decomposition of wood and detritus is challenging to most macroscopic organisms due to the recalcitrant nature of lignocellulose. Moreover, woody plants often protect themselves by synthesizing toxic or nocent compounds which infuse their tissues. Termites are essential wood decomposers in warmer terrestrial ecosystems and, as such, they have to cope with high concentrations of plant toxins in wood. In this paper, we evaluated the influence of wood age on the gut microbial (bacterial and fungal) communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) (Kollar, 1837) and Microcerotermes biroi (Termitidae) (Desneux, 1905). We confirmed that the secondary metabolite concentration decreased with wood age. We identified a core microbial consortium maintained in the gut of R. flavipes and M. biroi and found that its diversity and composition were not altered by the wood age. Therefore, the concentration of secondary metabolites had no effect on the termite gut microbiome. We also found that both termite feeding activities and wood age affect the wood microbiome. Whether the increasing relative abundance of microbes with termite activities is beneficial to the termites is unknown and remains to be investigated. IMPORTANCE Termites can feed on wood thanks to their association with their gut microbes. However, the current understanding of termites as holobiont is limited. To our knowledge, no studies comprehensively reveal the influence of wood age on the termite-associated microbial assemblage. The wood of many tree species contains high concentrations of plant toxins that can vary with their age and may influence microbes. Here, we studied the impact of Norway spruce wood of varying ages and terpene concentrations on the microbial communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) and Microcerotermes biroi (Termitidae). We performed a bacterial 16S rRNA and fungal ITS2 metabarcoding study to reveal the microbial communities associated with R. flavipes and M. biroi and their impact on shaping the wood microbiome. We noted that a stable core microbiome in the termites was unaltered by the feeding substrate, while termite activities influenced the wood microbiome, suggesting that plant secondary metabolites have negligible effects on the termite gut microbiome. Hence, our study shed new insights into the termite-associated microbial assemblage under the influence of varying amounts of terpene content in wood and provides a groundwork for future investigations for developing symbiont-mediated termite control measures.
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Affiliation(s)
- Amrita Chakraborty
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Kateřina Votýpková
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jaromír Hradecký
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Petr Stiblik
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jiří Synek
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Thomas Bourguignon
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
| | - Petr Baldrian
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Michael S. Engel
- American Museum of Natural History, New York, New York, USA
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Vojtěch Novotný
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Větrovský
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
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14
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Yang Y, Hu L, Li X, Wang J, Jin G. Nitrogen Fixation and Diazotrophic Community in Plastic-Eating Mealworms Tenebrio molitor L. MICROBIAL ECOLOGY 2023; 85:264-276. [PMID: 35061090 DOI: 10.1007/s00248-021-01930-5] [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: 06/15/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
Mealworms, the larvae of a coleopteran insect Tenebrio molitor L., are capable of eating, living on, and degrading non-hydrolyzable vinyl plastics as sole diet. However, vinyl plastics are carbon-rich but nitrogen-deficient. It remains puzzling how plastic-eating mealworms overcome the nutritional obstacle of nitrogen limitation. Here, we provide the evidence for nitrogen fixation activity within plastic-eating mealworms. Acetylene reduction assays illustrate that the nitrogen-fixing activity ranges from 12.3 ± 0.7 to 32.9 ± 9.3 nmol ethylene·h-1·gut-1 and the corresponding fixed nitrogen equivalents of protein are estimated as 8.6 to 23.0 µg per day per mealworm. Nature nitrogen isotopic analyses of plastic-eating mealworms provide further evidence for the assimilation of fixed nitrogen as a new nitrogen source. Eliminating the gut microbial microbiota with antibiotics impairs the mealworm's ability to fix nitrogen from the atmosphere, indicating the contribution of gut microbiota to nitrogen fixation. By using the traditional culture-dependent technique, PCR and RT-PCR of nifH gene, nitrogen-fixing bacteria diversity within the gut was detected, and the genus Klebsiella was demonstrated to be an important nitrogen-fixing symbiont. These findings first build the relationship between plastic degradation (carbon metabolism) and nitrogen fixation (nitrogen metabolism) within mealworms. Combined with previously reported plastic-degrading capability and nitrogen-fixing activity, mealworms may be potential candidates for up-recycling of plastic waste to produce protein sources.
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Affiliation(s)
- Yu Yang
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.
| | - Lin Hu
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Xiaoxi Li
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, People's Republic of China
| | - Jialei Wang
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Guishan Jin
- Analytical Laboratory, Beijing Research Institute of Uranium Geology, Beijing, 100029, People's Republic of China
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15
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Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas. mSystems 2022; 7:e0086422. [PMID: 36342154 PMCID: PMC9765461 DOI: 10.1128/msystems.00864-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transfer of animal and plant detritus of both terrestrial and marine origins to the deep sea occurs on a global scale. Microorganisms play an important role in mineralizing them therein, but these are yet to be identified in situ. To observe key bacteria involved, we conducted long-term in situ incubation and found that members of the family Marinifilaceae (MF) occurred as some of the most predominant bacteria thriving on the new inputs of plant and animal biomasses in the deep sea in both marginal and oceanic areas. This taxon is diverse and ubiquitous in marine environments. A total of 11 MAGs belonging to MF were retrieved from metagenomic data and diverged into four subgroups in the phylogenomic tree. Based on metagenomic and metatranscriptomic analyses, we described the metabolic features and in situ metabolizing activities of different subgroups. The MF-2 subgroup, which dominates plant detritus-enriched cultures, specializes in polysaccharide degradation and lignin oxidation and has high transcriptional activities of related genes in situ. Intriguingly, members of this subgroup encode a nitrogen fixation pathway to compensate for the shortage of nitrogen sources inside the plant detritus. In contrast, other subgroups dominating the animal tissue-supported microbiomes are distinguished from MF-2 with regard to carbon and nitrogen metabolism and exhibit high transcriptional activity for proteolysis in situ. Despite these metabolic divergences of MF lineages, they show high in situ transcriptional activities for organic fermentation and anaerobic respiration (reductions of metal and/or dimethyl sulfoxide). These results highlight the role of previously unrecognized Marinifilaceae bacteria in organic matter mineralization in marine environments by coupling carbon and nitrogen cycling with metal and sulfur. IMPORTANCE Microbial mineralization of organic matter has a significant impact on the global biogeochemical cycle. This report confirms the role of Marinifilaceae in organic degradation in the oceans, with a contribution to ocean carbon cycling that has previously been underestimated. It was the dominant taxon thriving on plant and animal biomasses in our in situ incubator, as well as in whale falls and wood falls. At least 9 subgroups were revealed, and they were widely distributed in oceans globally but predominant in organic-matter-rich environments, with an average relative abundance of 8.3%. Different subgroups display a preference for the degradation of different macromolecules (polysaccharides, lignin, and protein) and adapt to their environments via special metabolic mechanisms.
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16
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Matassa S, Boeckx P, Boere J, Erisman JW, Guo M, Manzo R, Meerburg F, Papirio S, Pikaar I, Rabaey K, Rousseau D, Schnoor J, Smith P, Smolders E, Wuertz S, Verstraete W. How can we possibly resolve the planet's nitrogen dilemma? Microb Biotechnol 2022; 16:15-27. [PMID: 36378579 PMCID: PMC9803332 DOI: 10.1111/1751-7915.14159] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/25/2022] [Accepted: 10/01/2022] [Indexed: 11/17/2022] Open
Abstract
Nitrogen is the most crucial element in the production of nutritious feeds and foods. The production of reactive nitrogen by means of fossil fuel has thus far been able to guarantee the protein supply for the world population. Yet, the production and massive use of fertilizer nitrogen constitute a major threat in terms of environmental health and sustainability. It is crucial to promote consumer acceptance and awareness towards proteins produced by highly effective microorganisms, and their potential to replace proteins obtained with poor nitrogen efficiencies from plants and animals. The fact that reactive fertilizer nitrogen, produced by the Haber Bosch process, consumes a significant amount of fossil fuel worldwide is of concern. Moreover, recently, the prices of fossil fuels have increased the cost of reactive nitrogen by a factor of 3 to 5 times, while international policies are fostering the transition towards a more sustainable agro-ecology by reducing mineral fertilizers inputs and increasing organic farming. The combination of these pressures and challenges opens opportunities to use the reactive nitrogen nutrient more carefully. Time has come to effectively recover used nitrogen from secondary resources and to upgrade it to a legal status of fertilizer. Organic nitrogen is a slow-release fertilizer, it has a factor of 2.5 or higher economic value per unit nitrogen as fertilizer and thus adequate technologies to produce it, for instance by implementing photobiological processes, are promising. Finally, it appears wise to start the integration in our overall feed and food supply chains of the exceptional potential of biological nitrogen fixation. Nitrogen produced by the nitrogenase enzyme, either in the soil or in novel biotechnology reactor systems, deserves to have a 'renaissance' in the context of planetary governance in general and the increasing number of people who desire to be fed in a sustainable way in particular.
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Affiliation(s)
- Silvio Matassa
- Department of Civil, Architectural and Environmental EngineeringUniversity of Naples Federico IINaplesItaly
| | - Pascal Boeckx
- Department of Green Chemistry and Technology, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Jos Boere
- Allied Waters B.V.NieuwegeinThe Netherlands
| | - Jan Willem Erisman
- Institute of Environmental SciencesLeiden UniversityLeidenThe Netherlands
| | - Miao Guo
- Department of Engineering, Faculty of Natural, Mathematical and Engineering SciencesKing's College LondonLondonUK
| | - Raffaele Manzo
- Department of Civil, Architectural and Environmental EngineeringUniversity of Naples Federico IINaplesItaly
| | | | - Stefano Papirio
- Department of Civil, Architectural and Environmental EngineeringUniversity of Naples Federico IINaplesItaly
| | - Ilje Pikaar
- School of Civil EngineeringThe University of QueenslandBrisbaneQueenslandAustralia
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Diederik Rousseau
- Department of Green Chemistry and Technology, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Jerald Schnoor
- Department of Civil and Environmental EngineeringUniversity of IowaIowa CityIowaUSA
| | - Peter Smith
- Institute of Biological and Environmental SciencesUniversity of AberdeenAberdeenUK
| | - Erik Smolders
- Division Soil and Water ManagementKatholieke Universiteit LeuvenLeuvenBelgium
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological UniversitySingaporeSingapore,School of Civil and Environmental Engineering, Nanyang Technological UniversitySingaporeSingapore
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
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17
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Li DD, Li JY, Hu ZQ, Liu TX, Zhang SZ. Fall Armyworm Gut Bacterial Diversity Associated with Different Developmental Stages, Environmental Habitats, and Diets. INSECTS 2022; 13:insects13090762. [PMID: 36135463 PMCID: PMC9503601 DOI: 10.3390/insects13090762] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 05/12/2023]
Abstract
The fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), is a major invasive pest that seriously threatens world agricultural production and food security. Microorganisms play a crucial role in the growth and development of insects. However, the diversity and dynamics of gut microbes with different developmental stages, environmental habitats, and diets in S. frugiperda remain unclear. In this study, we found the changes of the microbiome of S. frugiperda across their life stages, and the bacteria were dominated by Firmicutes and Proteobacteria. The community composition of the egg stage was quite different from other developmental stages, which had the highest community diversity and community richness, and was dominated by Proteobacteria. The bacterial community compositions of male and female adults were similar to those of early larvae stage (L1-L2), and operational taxonomic units (OTUs) with abundant content were Enterococcus and Enterobacteriaceae bacteria, including Enterobacteria, Klebsiella, Pantoea, and Escherichia. The third instar larvae (L3) mainly consist of Enterococcus. The late stage larvae (L4-L6) harbored high proportions of Enterococcus, Rhodococcus, and Ralstonia. There was no significant difference in gut microbial composition between field populations and laboratory populations in a short period of rearing time. However, after long-term laboratory feeding, the gut microbial diversity of S. frugiperda was significantly reduced. Enterococcus and Rhodococccus of S. frugiperda feeding on maize showed higher relative proportion, while the microbial community of S. frugiperda feeding on artificial diet was composed mainly of Enterococcus, with a total of 98% of the gut microbiota. The gene functions such as metabolism, cell growth and death, transport and catabolism, and environmental adaptation were more active in S. frugiperda feeding on corn than those feeding on artificial diet. In short, these results indicate that developmental stage, habitat, and diet can alter the gut bacteria of S. frugiperda, and suggest a vertical transmission route of bacteria in S. frugiperda. A comprehensive understanding of gut microbiome of S. frugiperda will help develop novel pest control strategies to manage this pest.
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18
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Arora J, Kinjo Y, Šobotník J, Buček A, Clitheroe C, Stiblik P, Roisin Y, Žifčáková L, Park YC, Kim KY, Sillam-Dussès D, Hervé V, Lo N, Tokuda G, Brune A, Bourguignon T. The functional evolution of termite gut microbiota. MICROBIOME 2022; 10:78. [PMID: 35624491 PMCID: PMC9137090 DOI: 10.1186/s40168-022-01258-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/16/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of termite gut microbiota. RESULTS We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that essential nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways. CONCLUSIONS Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ~ 150 million years ago. Therefore, the "world's smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception. Video Abstract.
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Affiliation(s)
- Jigyasa Arora
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
| | - Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Aleš Buček
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Crystal Clitheroe
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Petr Stiblik
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Yves Roisin
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Lucia Žifčáková
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Ki Yoon Kim
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - David Sillam-Dussès
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology, LEEC, UR 4443, Villetaneuse, France
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Gaku Tokuda
- Tropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic.
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Pan J, Xu W, Zhou Z, Shao Z, Dong C, Liu L, Luo Z, Li M. Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge. MICROBIOME 2022; 10:8. [PMID: 35045876 PMCID: PMC8767757 DOI: 10.1186/s40168-021-01202-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/24/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field. RESULTS In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields. CONCLUSIONS This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.
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Affiliation(s)
- Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Zhichao Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Chunming Dong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
- School of Marine Sciences, Nanjing University of Information Science & Technology, 210044 Nanjing, People’s Republic of China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
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20
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Ecological Role of Bacteria Involved in the Biogeochemical Cycles of Mangroves Based on Functional Genes Detected through GeoChip 5.0. mSphere 2022; 7:e0093621. [PMID: 35019668 PMCID: PMC8754168 DOI: 10.1128/msphere.00936-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mangroves provide a variety of ecosystem services and contribute greatly to the global biogeochemical cycle. Microorganisms play important roles in biogeochemical cycles and maintain the dynamic balance of mangroves. However, the roles of bacteria in the biogeochemical cycles of mangroves and their ecological distribution and functions remain largely uncharacterized. This study thus sought to analyze and compare the ecological distributions and potential roles of bacteria in typical mangroves using 16S rRNA gene amplicon sequencing and GeoChip. Interestingly, the bacterial community compositions were largely similar in the studied mangroves, including Shenzhen, Yunxiao, Zhanjiang, Hainan, Hongkong, Fangchenggang, and Beihai mangroves. Moreover, gamma-proteobacterium_uncultured and Woeseia were the most abundant microorganisms in the mangroves. Furthermore, most of the bacterial communities were significantly correlated with phosphorus levels (P < 0.05; −0.93 < R < 0.93), suggesting that this nutrient is a vital driver of bacterial community composition. Additionally, GeoChip analysis indicated that the functional genes amyA, narG, dsrA, and ppx were highly abundant in the studied mangroves, suggesting that carbon degradation, denitrification, sulfite reduction, and polyphosphate degradation are crucial processes in typical mangroves. Moreover, several genera were found to synergistically participate in biogeochemical cycles in mangroves. For instance, Neisseria, Ruegeria, Rhodococcus, Desulfotomaculum, and Gordonia were synergistically involved in the carbon, nitrogen, and sulfur cycles, whereas Neisseria and Treponema were synergistically involved in the nitrogen cycle and the sulfur cycle. Taken together, our findings provide novel insights into the ecological roles of bacteria in the biogeochemical cycles of mangroves. IMPORTANCE Bacteria have important functions in biogeochemical cycles, but studies on their function in an important ecosystem, mangroves, are still limited. Here, we investigated the ecological role of bacteria involved in biogeochemical cycles in seven representative mangroves of southern China. Furthermore, various functional genes from bacteria involved in biogeochemical cycles were identified by GeoChip 5.0. The functional genes associated with the carbon cycle (particularly carbon degradation) were the most abundant, suggesting that carbon degradation is the most active process in mangroves. Additionally, some high-abundance bacterial populations were found to synergistically mediate key biogeochemical cycles in the mangroves, including Neisseria, Pseudomonas, Treponema, Desulfotomaculum, and Nitrosospira. In a word, our study gives novel insights into the function of bacteria in biogeochemical cycles in mangroves.
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21
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Park K, Lee H. Can flushing gas distort the rumen in vitro experiment results? Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Tongununui P, Kuriya Y, Murata M, Sawada H, Araki M, Nomura M, Morioka K, Ichie T, Ikejima K, Adachi K. Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling. PLoS One 2022; 16:e0261654. [PMID: 34972143 PMCID: PMC8719709 DOI: 10.1371/journal.pone.0261654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/07/2021] [Indexed: 11/29/2022] Open
Abstract
Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in material flow in carbon-rich and nitrogen-limited mangrove ecosystems; however, the process of assimilation and conversion into detritus has not been well studied. In this study, we performed microbiome analyses of intestinal bacteria from three species of mangrove crab and five sediment positions in the mud lobster mounds, including the crab burrow wall, to study the interactive roles of crabs and sediment in metabolism. Metagenome analysis revealed species-dependent intestinal profiles, especially in Neosarmatium smithi, while the sediment microbiome was similar in all positions, albeit with some regional dependency. The microbiome profiles of crab intestines and sediments were significantly different in the MDS analysis based on OTU similarity; however, 579 OTUs (about 70% of reads in the crab intestinal microbiome) were identical between the intestinal and sediment bacteria. In the phenotype prediction, cellulose degradation was observed in the crab intestine. Cellulase activity was detected in both crab intestine and sediment. This could be mainly ascribed to Demequinaceae, which was predominantly found in the crab intestines and burrow walls. Nitrogen fixation was also enriched in both the crab intestines and sediments, and was supported by the nitrogenase assay. Similar to earlier reports, sulfur-related families were highly enriched in the sediment, presumably degrading organic compounds as terminal electron acceptors under anaerobic conditions. These results suggest that mangrove crabs and habitat sediment both contribute to carbon and nitrogen cycling in the mangrove ecosystem via these two key reactions.
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Affiliation(s)
- Prasert Tongununui
- Department of Marine Science and Environment, Faculty of Science and Fisheries Technology, Rajamangala University of Technology Srivijaya, Tambon Maifad, Amphur Sikao, Trang, Thailand
| | - Yuki Kuriya
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Masahiro Murata
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Hideki Sawada
- Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Maizuru, Kyoto, Japan
| | - Michihiro Araki
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Tokyo, Japan
| | - Mika Nomura
- Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Katsuji Morioka
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Tomoaki Ichie
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Kou Ikejima
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Kohsuke Adachi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
- * E-mail:
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23
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Mohr W, Lehnen N, Ahmerkamp S, Marchant HK, Graf JS, Tschitschko B, Yilmaz P, Littmann S, Gruber-Vodicka H, Leisch N, Weber M, Lott C, Schubert CJ, Milucka J, Kuypers MMM. Terrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium. Nature 2021; 600:105-109. [PMID: 34732889 PMCID: PMC8636270 DOI: 10.1038/s41586-021-04063-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/22/2021] [Indexed: 01/23/2023]
Abstract
Symbiotic N2-fixing microorganisms have a crucial role in the assimilation of nitrogen by eukaryotes in nitrogen-limited environments1-3. Particularly among land plants, N2-fixing symbionts occur in a variety of distantly related plant lineages and often involve an intimate association between host and symbiont2,4. Descriptions of such intimate symbioses are lacking for seagrasses, which evolved around 100 million years ago from terrestrial flowering plants that migrated back to the sea5. Here we describe an N2-fixing symbiont, 'Candidatus Celerinatantimonas neptuna', that lives inside seagrass root tissue, where it provides ammonia and amino acids to its host in exchange for sugars. As such, this symbiosis is reminiscent of terrestrial N2-fixing plant symbioses. The symbiosis between Ca. C. neptuna and its host Posidonia oceanica enables highly productive seagrass meadows to thrive in the nitrogen-limited Mediterranean Sea. Relatives of Ca. C. neptuna occur worldwide in coastal ecosystems, in which they may form similar symbioses with other seagrasses and saltmarsh plants. Just like N2-fixing microorganisms might have aided the colonization of nitrogen-poor soils by early land plants6, the ancestors of Ca. C. neptuna and its relatives probably enabled flowering plants to invade nitrogen-poor marine habitats, where they formed extremely efficient blue carbon ecosystems7.
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Affiliation(s)
- Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Nadine Lehnen
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | | | - Jon S Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Pelin Yilmaz
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Data Science Research Group, Institute for Artificial Intelligence in Medicine, University Hospital Essen, Essen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Nikolaus Leisch
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | | | - Carsten J Schubert
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Department of Surface Waters-Research and Management, Kastanienbaum, Switzerland
| | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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24
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Koch RA, Yoon GM, Aryal UK, Lail K, Amirebrahimi M, LaButti K, Lipzen A, Riley R, Barry K, Henrissat B, Grigoriev IV, Herr JR, Aime MC. Symbiotic nitrogen fixation in the reproductive structures of a basidiomycete fungus. Curr Biol 2021; 31:3905-3914.e6. [PMID: 34245690 DOI: 10.1016/j.cub.2021.06.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/09/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022]
Abstract
Nitrogen (N) fixation is a driving force for the formation of symbiotic associations between N2-fixing bacteria and eukaryotes.1 Limited examples of these associations are known in fungi, and none with sexual structures of non-lichenized species.2-6 The basidiomycete Guyanagaster necrorhizus is a sequestrate fungus endemic to the Guiana Shield.7 Like the root rot-causing species in its sister genera Armillaria and Desarmillaria, G. necrorhizus sporocarps fruit from roots of decaying trees (Figures 1A-1C),8 and genome sequencing is consistent with observations that G. necrorhizus is a white-rotting decomposer. This species also represents the first documentation of an arthropod-dispersed sequestrate fungus. Numerous species of distantly related wood-feeding termites, which scavenge for N-rich food, feed on the mature spore-bearing tissue, or gleba, of G. necrorhizus. During feeding, mature spores adhere to termites for subsequent dispersal.9 Using chemical assays, isotope analysis, and high-throughput sequencing, we show that the sporocarps harbor actively N2-fixing Enterobacteriaceae species and that the N content within fungal tissue increases with maturation. Untargeted proteomic profiling suggests that ATP generation in the gleba is accomplished via fermentation. The use of fermentation-an anaerobic process-indicates that the sporocarp environment is anoxic, likely an adaptation to protect the oxygen-sensitive nitrogenase enzyme. Sporocarps also have a thick outer covering, possibly to limit oxygen diffusion. The enriched N content within mature sporocarps may offer a dietary inducement for termites in exchange for spore dispersal. These results show that the flexible metabolic capacity of fungi may facilitate N2-fixing associations, as well as higher-level organismal associations.
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Affiliation(s)
- Rachel A Koch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; Department of Plant Pathology, University of Nebraska, Lincoln, NE 68520, USA.
| | - Gyeong Mee Yoon
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mojgan Amirebrahimi
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille 13288, France; Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille 13288, France; Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Joshua R Herr
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68520, USA; Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68520, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
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O'Brien PA, Andreakis N, Tan S, Miller DJ, Webster NS, Zhang G, Bourne DG. Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts. Mol Ecol 2021; 30:3768-3782. [PMID: 34060182 DOI: 10.1111/mec.16006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group. Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle key microbial interactions that occur within complex microbiomes and reveal long-standing, essential microbial symbioses in coral reef invertebrates.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Nikos Andreakis
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Qld, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Qld, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Qld, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia
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Song Y, Hervé V, Radek R, Pfeiffer F, Zheng H, Brune A. Characterization and phylogenomic analysis of Breznakiella homolactica gen. nov. sp. nov. indicate that termite gut treponemes evolved from non-acetogenic spirochetes in cockroaches. Environ Microbiol 2021; 23:4228-4245. [PMID: 33998119 DOI: 10.1111/1462-2920.15600] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 01/01/2023]
Abstract
Spirochetes of the genus Treponema are surprisingly abundant in termite guts, where they play an important role in reductive acetogenesis. Although they occur in all termites investigated, their evolutionary origin is obscure. Here, we isolated the first representative of 'termite gut treponemes' from cockroaches, the closest relatives of termites. Phylogenomic analysis revealed that Breznakiella homolactica gen. nov. sp. nov. represents the most basal lineage of the highly diverse 'termite cluster I', a deep-branching sister group of Treponemataceae (fam. 'Termitinemataceae') that was present already in the cockroach ancestor of termites and subsequently coevolved with its host. Breznakiella homolactica is obligately anaerobic and catalyses the homolactic fermentation of both hexoses and pentoses. Resting cells produced acetate in the presence of oxygen. Genome analysis revealed the presence of pyruvate oxidase and catalase, and a cryptic potential for the formation of acetate, ethanol, formate, CO2 and H2 - the fermentation products of termite gut isolates. Genes encoding key enzymes of reductive acetogenesis, however, are absent, confirming the hypothesis that the ancestral metabolism of the cluster was fermentative, and that the capacity for acetogenesis from H2 plus CO2 - the most intriguing property among termite gut treponemes - was acquired by lateral gene transfer.
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Affiliation(s)
- Yulin Song
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Renate Radek
- Institute of Biology/Zoology, Free University of Berlin, Königin-Luise-Str. 1-3, Berlin, 14195, Germany
| | - Fabienne Pfeiffer
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Hao Zheng
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
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Tokuda G. Origin of symbiotic gut spirochetes as key players in the nutrition of termites. Environ Microbiol 2021; 23:4092-4097. [PMID: 34097340 DOI: 10.1111/1462-2920.15625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/17/2022]
Abstract
Termites harbour symbiotic spirochetes in their hindguts, which have long been considered treponemes, although they represent separate lines of descent from known species of Treponema. 'Termite gut treponemes' have a mutualistic relationship with the host termites with their physiological properties including CO2 -reductive acetogenesis, from which the resulting acetate fulfils most of the respiratory requirement of the host. Song and co-workers showed that a spirochetal isolate (strain RmG30) from a Madeira cockroach represents the earliest branching lineage of extremely diverse termite (Treponema) cluster I and was a simple homolactic fermenter, suggesting that CO2 -reductive acetogenesis exhibited by some members of termite cluster I originated via horizontal gene transfer. Phylogenomic and 16S rRNA sequence-based phylogenetic analyses indicated a deeply-branched sister clade containing termite cluster I was distinguishable as a family-level lineage. In this context, a new family, 'Termitinemataceae' has been proposed for this clade. Strain RmG30 has been designated as the type strain of Breznakiella homolactica gen. nov. sp. nov. named after John A. Breznak, an American microbiologist distinguished in termite gut microbiology. The study has posed important questions for the future, including the actual roles of the termite spirochetes in each termite lineage and the evolutionary process of their physiological properties.
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Affiliation(s)
- Gaku Tokuda
- Tropical Biosphere Research Center, COMB, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, Japan
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Vikram S, Arneodo JD, Calcagno J, Ortiz M, Mon ML, Etcheverry C, Cowan DA, Talia P. Diversity structure of the microbial communities in the guts of four neotropical termite species. PeerJ 2021; 9:e10959. [PMID: 33868801 PMCID: PMC8035897 DOI: 10.7717/peerj.10959] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/27/2021] [Indexed: 01/04/2023] Open
Abstract
The termite gut microbiome is dominated by lignocellulose degrading microorganisms. This study describes the intestinal microbiota of four Argentinian higher termite species with different feeding habits: Microcerotermes strunckii (hardwood), Nasutitermes corniger (softwood), Termes riograndensis (soil organic matter/grass) and Cornitermes cumulans (grass) by deep sequencing of amplified 16S rRNA and ITS genes. In addition, we have performed a taxonomic and gut community structure comparison incorporating into the analysis the previously reported microbiomes of additional termite species with varied diets. The bacterial phylum Spirochaetes was dominant in the guts of M. strunckii, N. corniger and C. cumulans, whereas Firmicutes predominated in the T. riograndensis gut microbiome. A single bacterial genus, Treponema (Spirochaetes), was dominant in all termite species, except for T. riograndensis. Both in our own sequenced samples and in the broader comparison, prokaryotic α-diversity was higher in the soil/grass feeders than in the wood feeders. Meanwhile, the β-diversity of prokaryotes and fungi was highly dissimilar among strict wood-feeders, whereas that of soil- and grass-feeders grouped more closely. Ascomycota and Basidiomycota were the only fungal phyla that could be identified in all gut samples, because of the lack of reference sequences in public databases. In summary, higher microbial diversity was recorded in termites with more versatile feeding sources, providing further evidence that diet, along with other factors (e.g., host taxonomy), influences the microbial community assembly in the termite gut.
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Affiliation(s)
- Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Joel D Arneodo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Javier Calcagno
- Centro de Ciencias Naturales, Ambientales y Antropológicas, Universidad Maimonides (CCNAA), CABA, Argentina
| | - Maximiliano Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Maria Laura Mon
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Clara Etcheverry
- Biología de los Invertebrados, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Paola Talia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
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Marzocchi U, Bonaglia S, Zaiko A, Quero GM, Vybernaite-Lubiene I, Politi T, Samuiloviene A, Zilius M, Bartoli M, Cardini U. Zebra Mussel Holobionts Fix and Recycle Nitrogen in Lagoon Sediments. Front Microbiol 2021; 11:610269. [PMID: 33542710 PMCID: PMC7851879 DOI: 10.3389/fmicb.2020.610269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Bivalves are ubiquitous filter-feeders able to alter ecosystems functions. Their impact on nitrogen (N) cycling is commonly related to their filter-feeding activity, biodeposition, and excretion. A so far understudied impact is linked to the metabolism of the associated microbiome that together with the host constitute the mussel's holobiont. Here we investigated how colonies of the invasive zebra mussel (Dreissena polymorpha) alter benthic N cycling in the shallow water sediment of the largest European lagoon (the Curonian Lagoon). A set of incubations was conducted to quantify the holobiont's impact and to quantitatively compare it with the indirect influence of the mussel on sedimentary N transformations. Zebra mussels primarily enhanced the recycling of N to the water column by releasing mineralized algal biomass in the form of ammonium and by stimulating dissimilatory nitrate reduction to ammonium (DNRA). Notably, however, not only denitrification and DNRA, but also dinitrogen (N2) fixation was measured in association with the holobiont. The diazotrophic community of the holobiont diverged substantially from that of the water column, suggesting a unique niche for N2 fixation associated with the mussels. At the densities reported in the lagoon, mussel-associated N2 fixation may account for a substantial (and so far, overlooked) source of bioavailable N. Our findings contribute to improve our understanding on the ecosystem-level impact of zebra mussel, and potentially, of its ability to adapt to and colonize oligotrophic environments.
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Affiliation(s)
- Ugo Marzocchi
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Center for Water Technology (WATEC), Department of Biology, Aarhus University, Aarhus, Denmark
| | - Stefano Bonaglia
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anastasija Zaiko
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Grazia M. Quero
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Institute for Biological Resources and Marine Biotechnologies, National Research Council of Italy, Ancona, Italy
| | | | - Tobia Politi
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
| | | | - Mindaugas Zilius
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Marco Bartoli
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Chemistry, Life science and Environmental Sustainability, Parma University, Parma, Italy
| | - Ulisse Cardini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
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Gomes Carvalho Alves KL, Granja-Salcedo YT, Messana JD, Carneiro de Souza V, Generoso Ganga MJ, Detogni Colovate PH, Kishi LT, Berchielli TT. Rumen bacterial diversity in relation to nitrogen retention in beef cattle. Anaerobe 2020; 67:102316. [PMID: 33383197 DOI: 10.1016/j.anaerobe.2020.102316] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/10/2020] [Accepted: 12/21/2020] [Indexed: 02/02/2023]
Abstract
This study aimed to characterize the rumen bacterial diversity of beef steers differing in the efficiency of nitrogen retention (ENR). Eight castrated steers and fitted with ruminal silicone - and duodenal T-type cannulas were used in a cross-over design with three consecutive periods and three diets. During each experimental period, nitrogen balance was measured, and based on the efficiency of N utilization data, steers were split into three ENR groups: high (HNR, 56.6% ± 3.3%, n = 10), medium (MNR, 45.8% ± 2.2%, n = 6), and low (LNR, 37.7% ± 1.9%, n = 8) using the NbClust package version 2.0.4 in R. Prevotellaceae, Lactobacillaceae, Leuconostocaceae, Clostridiales_Incertae_Sedis_XIII, Lachnospiraceae, and Peptostreptococcaceae were more abundant in LNR (P < 0.05) compared to HNR or MNR. Negative correlations were found between N retention and Mogibacterium, Anaerofustis, Butyrivibrio, Coprococcus, Hespellia, Lactonifactor and Lachnospiraceae (r ≤ -0.61; P ≤ 0.05). Prevotella, Hespellia, Lactonifactor, Lachnospiraceae_other, and Anaerobiospirillum were positively correlated between urinary N excretion (r > 0.55; P < 0.01), and negative correlations were found with Elusimicrobia, Victivallis and Treponema (r < -0.41; P < 0.05). The adjustment of the rumen bacterial community differed significantly between the N use retention groups. The high N retention in beef cattle was associated with less abundant bacteria in the rumen; however, N fixation capacity and uncharacterized rumen microorganisms need to be elucidated in future studies. In contrast, lower N utilization was associated with high abundance of bacteria that promote greater urinary N excretion through ruminal protein degradation.
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Affiliation(s)
- Kênia Larissa Gomes Carvalho Alves
- Department of Animal Science, School of Agrarian and Veterinarian Sciences, São Paulo State University - UNESP, Jaboticabal, SP, Brazil.
| | - Yury Tatiana Granja-Salcedo
- Department of Animal Science, School of Agrarian and Veterinarian Sciences, São Paulo State University - UNESP, Jaboticabal, SP, Brazil; Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, CI EI Nus, San Roque, Antioquía, Colombia
| | - Juliana Duarte Messana
- Department of Animal Science, School of Agrarian and Veterinarian Sciences, São Paulo State University - UNESP, Jaboticabal, SP, Brazil
| | - Vinícius Carneiro de Souza
- Department of Animal Science, School of Agrarian and Veterinarian Sciences, São Paulo State University - UNESP, Jaboticabal, SP, Brazil; Department of Dairy Science, Virginia Tech, Blacksburg, 24061, USA
| | - Maria Júlia Generoso Ganga
- Department of Animal Science, School of Agrarian and Veterinarian Sciences, São Paulo State University - UNESP, Jaboticabal, SP, Brazil
| | - Paulo Henrique Detogni Colovate
- Department of Animal Science, School of Agrarian and Veterinarian Sciences, São Paulo State University - UNESP, Jaboticabal, SP, Brazil
| | - Luciano Takeshi Kishi
- National Laboratory of Scientific Computing, Petrópolis, RJ, Brazil; Department of Technology, School of Agrarian and Veterinarian Sciences, São Paulo State University - UNESP, Jaboticabal, SP, Brazil
| | - Telma Teresinha Berchielli
- Department of Animal Science, School of Agrarian and Veterinarian Sciences, São Paulo State University - UNESP, Jaboticabal, SP, Brazil; INCT/CA-UFV-Department of Animal Science, Viçosa, MG, Brazil
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Cleary DFR, Polónia ARM, Reijnen BT, Berumen ML, de Voogd NJ. Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea. MICROBIAL ECOLOGY 2020; 80:103-119. [PMID: 31932882 DOI: 10.1007/s00248-019-01465-w] [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: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.
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Affiliation(s)
- D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - B T Reijnen
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, The Netherlands
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Mahadevan P, Middlebrooks ML. Bacterial diversity in the clarki ecotype of the photosynthetic sacoglossan, Elysia crispata. Microbiologyopen 2020; 9:e1098. [PMID: 32602643 PMCID: PMC7520991 DOI: 10.1002/mbo3.1098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/25/2020] [Accepted: 05/30/2020] [Indexed: 01/04/2023] Open
Abstract
Few studies have examined the bacterial communities associated with photosynthetic sacoglossan sea slugs. In this study, we determined the bacterial diversity in the clarki ecotype, Elysia crispata using 16S rRNA sequencing. Computational analysis using QIIME2 revealed variability between individual samples, with the Spirochaetes and Bacteroidetes phyla dominating most samples. Tenericutes and Proteobacteria were also found, among other phyla. Computational metabolic profiling of the bacteria revealed a variety of metabolic pathways involving carbohydrate metabolism, lipid metabolism, nucleotide metabolism, and amino acid metabolism. Although associated bacteria may be involved in mutually beneficial metabolic pathways, there was a high degree of variation in the bacterial community of individual slugs. This suggests that many of these relationships are likely opportunistic rather than obligate and that many of these bacteria may live commensally providing no major benefit to the slugs.
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Exploring the effect of plant substrates on bacterial community structure in termite fungus-combs. PLoS One 2020; 15:e0232329. [PMID: 32357167 PMCID: PMC7194444 DOI: 10.1371/journal.pone.0232329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 04/14/2020] [Indexed: 11/19/2022] Open
Abstract
Fungus-cultivating termites are successful herbivores largely rely on the external symbiotic fungus-combs to decompose plant polysaccharides. The comb harbors both fungi and bacteria. However, the complementary roles and functions of the bacteria are out of the box. To this purpose, we look into different decomposition stages of fungus-combs using high-throughput sequencing of the 16S rRNA gene to examine bacterial community structure. We also explored the bacterial response to physicochemical indexes (such as moisture, ash content and organic matter) and plant substrates (leaves or branches or mix food). Some specific families such as Lachnospiraceae, Ruminococcaceae, and Peptostreptococcaceae may be involved in lignocellulose degradation, whereas Burkholderiaceae may be associated with aromatic compounds degradation. We observed that as the comb mature there is a shift of community composition which may be an adjustment of specific bacteria to deal with different lignocellulosic material. Our results indicated that threshold amount of physicochemical indexes are beneficial for bacterial diversity but too high moisture, low organic matter and high ash content may reduce their diversity. Furthermore, the average highest bacterial diversity was recorded from the comb built by branches followed by mix food and leaves. Besides, this study could help in the use of bacteria from the comb of fungus-cultivating termites in forestry and agricultural residues making them easier to digest as fodder.
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Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes. Sci Rep 2020; 10:3864. [PMID: 32123275 PMCID: PMC7052144 DOI: 10.1038/s41598-020-60850-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/24/2019] [Indexed: 11/08/2022] Open
Abstract
In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.
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Schwob G, Cabrol L, Poulin E, Orlando J. Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii. Front Microbiol 2020; 11:308. [PMID: 32184772 PMCID: PMC7058685 DOI: 10.3389/fmicb.2020.00308] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/11/2020] [Indexed: 12/25/2022] Open
Abstract
Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition and putative functional capacity, evaluating its differentiation among the gut content and the gut tissue in comparison with the external sediment. Additionally, we aimed to define a core gut microbiota between A. agassizii populations to identify potential keystone bacterial taxa. Our results show that the diversity and the composition of the microbiota, at both genetic and predicted functional levels, were mostly driven by the sample type, and to a lesser extent by the population location. Specific bacterial taxa, belonging mostly to Planctomycetacia and Spirochaetia, were differently enriched in the gut content and the gut tissue, respectively. Predictive functional profiles revealed higher abundance of specific pathways, as the sulfur cycle in the gut content and the amino acid metabolism, in the gut tissue. Further, the definition of a core microbiota allowed to obtain evidence of specific localization of bacterial taxa and the identification of potential keystone taxa assigned to the Desulfobacula and Spirochaeta genera as potentially host selected. The ecological relevance of these keystone taxa in the host metabolism is discussed.
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Affiliation(s)
- Guillaume Schwob
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Léa Cabrol
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
| | - Elie Poulin
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Zeng W, Liu B, Zhong J, Li Q, Li Z. A Natural High-Sugar Diet Has Different Effects on the Prokaryotic Community Structures of Lower and Higher Termites (Blattaria). ENVIRONMENTAL ENTOMOLOGY 2020; 49:21-32. [PMID: 31782953 DOI: 10.1093/ee/nvz130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 06/10/2023]
Abstract
The lignocellulosic digestive symbiosis in termites is a dynamic survival adaptation system. While the contribution of hereditary and habitat factors to the development of the symbiotic bacterial community of termites had been confirmed, the manner in which these factors affect functional synergism among different bacterial lineages has still not been fully elucidated. Therefore, the 16S rRNA gene libraries of Odontotermes formosanus Shiraki (Blattodea: Termitidae) and Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) sampled from sugarcane fields (high sugar) or pine tree forests (no free sugar) were sequenced. The results verify that the prokaryotic community structures of termites could be significantly reshaped by native dietary isolation within a species. Although the most dominant phyla are convergent in all samples, their relative abundances in these two termite species exhibited a reverse variation pattern when the termite hosts were fed on the high-sugar diet. Furthermore, we showed that the taxonomic composition of the dominant phyla at the family or genus level differentiate depending on the diet and the host phylogeny. We hypothesize that the flexible bacterial assemblages at low taxonomic level might exert variable functional collaboration to accommodate to high-sugar diet. In addition, the functional predictions of Tax4Fun suggest a stable metabolic functional structure of the microbial communities of the termites in both different diet habitats and taxonomy. We propose that the symbiotic bacterial community in different host termites developed a different functional synergistic pattern, which may be essential to maintain the stability of the overall metabolic function for the survival of termites.
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Affiliation(s)
- Wenhui Zeng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Bingrong Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Junhong Zhong
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Qiujian Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Zhiqiang Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
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Kaya D, Kjellerup BV, Chourey K, Hettich RL, Taggart DM, Löffler FE. Impact of Fixed Nitrogen Availability on Dehalococcoides mccartyi Reductive Dechlorination Activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14548-14558. [PMID: 31693350 DOI: 10.1021/acs.est.9b04463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biostimulation to promote reductive dechlorination is widely practiced, but the value of adding an exogenous nitrogen (N) source (e.g., NH4+) during treatment is unclear. This study investigates the effect of NH4+ availability on organohalide-respiring Dehalococcoides mccartyi (Dhc) growth and reductive dechlorination in enrichment cultures derived from groundwater (PW4) and river sediment (TC) impacted with chlorinated ethenes. In PW4 cultures, the addition of NH4+ increased cis-1,2-dichloroethene (cDCE)-to-ethene dechlorination rates about 5-fold (20.6 ± 1.6 versus 3.8 ± 0.5 μM Cl- d-1), and the total number of Dhc 16S rRNA gene copies were about 43-fold higher in incubations with NH4+ ((1.8 ± 0.9) × 108 mL-1) compared to incubations without NH4+ ((4.1 ± 0.8) × 107 mL-1). In TC cultures, NH4+ also stimulated cDCE-to-ethene dechlorination and Dhc growth. Quantitative polymerase chain reaction (qPCR) revealed that Cornell-type Dhc capable of N2 fixation dominated PW4 cultures without NH4+, but their relative abundance decreased in cultures with NH4+ amendment (i.e., 99 versus 54% of total Dhc). Pinellas-type Dhc incapable of N2 fixation were responsible for cDCE dechlorination in TC cultures, and diazotrophic community members met their fixed N requirement in the medium without NH4+. Responses to NH4+ were apparent at the community level, and N2-fixing bacterial populations increased in incubations without NH4+. Quantitative assessment of Dhc nitrogenase genes, transcripts, and proteomics data linked Cornell-type Dhc nifD and nifK expression with fixed N limitation. NH4+ additions also demonstrated positive effects on Dhc in situ dechlorination activity in the vicinity of well PW4. These findings demonstrate that biostimulation with NH4+ can enhance Dhc reductive dechlorination rates; however, a "do nothing" approach that relies on indigenous diazotrophs can achieve similar dechlorination end points and avoids the potential for stalled dechlorination due to inhibitory levels of NH4+ or transformation products (i.e., nitrous oxide).
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Affiliation(s)
- Devrim Kaya
- Biosciences Division and ⊥Chemical Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Department of Civil and Environmental Engineering , University of Maryland College Park , College Park , Maryland 20742 , United States
| | - Birthe V Kjellerup
- Department of Civil and Environmental Engineering , University of Maryland College Park , College Park , Maryland 20742 , United States
| | | | | | - Dora M Taggart
- Microbial Insights, Inc. , Knoxville , Tennessee 37932 , United States
| | - Frank E Löffler
- Biosciences Division and ⊥Chemical Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
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Waidele L, Korb J, Voolstra CR, Dedeine F, Staubach F. Ecological specificity of the metagenome in a set of lower termite species supports contribution of the microbiome to adaptation of the host. Anim Microbiome 2019; 1:13. [PMID: 33499940 PMCID: PMC7807685 DOI: 10.1186/s42523-019-0014-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/23/2019] [Indexed: 12/27/2022] Open
Abstract
Background Elucidating the interplay between hosts and their microbiomes in ecological adaptation has become a central theme in evolutionary biology. A textbook example of microbiome-mediated adaptation is the adaptation of lower termites to a wood-based diet, as they depend on their gut microbiome to digest wood. Lower termites have further adapted to different life types. Termites of the wood-dwelling life type never leave their nests and feed on a uniform diet. Termites of the foraging life type forage for food outside the nest and have access to other nutrients. Here we sought to investigate whether the microbiome that is involved in food substrate breakdown and nutrient acquisition might contribute to adaptation to these dietary differences. We reasoned that this should leave ecological imprints on the microbiome. Results We investigated the protist and bacterial microbiomes of a total of 29 replicate colonies from five termite species, covering both life types, using metagenomic shotgun sequencing. The microbiome of wood-dwelling species with a uniform wood diet was enriched for genes involved in lignocellulose degradation. Furthermore, metagenomic patterns suggest that the microbiome of wood-dwelling species relied primarily on direct fixation of atmospheric nitrogen, while the microbiome of foraging species entailed the necessary pathways to utilize nitrogen in the form of nitrate for example from soil. Conclusion Our findings are consistent with the notion that the microbiome of wood-dwelling species bears an imprint of its specialization on degrading a uniform wood diet, while the microbiome of the foraging species might reflect its adaption to access growth limiting nutrients from more diverse sources. This supports the idea that specific subsets of functions encoded by the microbiome can contribute to host adaptation.
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Affiliation(s)
- Lena Waidele
- Biologie I, University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany
| | - Judith Korb
- Biologie I, University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany
| | | | - Franck Dedeine
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, 37200, Tours, France
| | - Fabian Staubach
- Biologie I, University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany.
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Yang QS, Dong JD, Ahmad M, Ling J, Zhou WG, Tan YH, Zhang YZ, Shen DD, Zhang YY. Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs. BMC Microbiol 2019; 19:188. [PMID: 31416417 PMCID: PMC6694519 DOI: 10.1186/s12866-019-1565-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor their nitrogenase transcriptional activity are well-understood. In this study, we used nifH gene Illumina sequencing and quantitative PCR to characterize the community composition and nifH expression profile of PADs with > 100 μm size fraction in the euphotic zone of the northern South China Sea. RESULTS The results of DNA- and RNA-derived nifH gene revealed a higher alpha-diversity in the active than in the total community. Moreover, the compositional resemblance among different sites was less for active than for total communities of PADs. We characterized the 20 most abundant OTUs by ranking the sum of sequence reads across 9 sampling stations for individual OTUs in both nifH DNA and RNA libraries, and then assessed their phylogenetic relatedness. Eight of the 20 abundant OTUs were phylogenetically affiliated with Trichodesmium and occurred in approximately equal proportion in both the DNA and RNA libraries. The analysis of nifH gene expression level showed uneven attribute of the abundance and nitrogenase activities by the remaining 12 OTUs. Taxa belonging to cluster III and Betaproteobacteria were present at moderate abundance but exhibited negligible nitrogenase transcription activity. Whereas, the abundances of Richelia, Deltaproteobacteria and Gammaproteobacteria were low but the contribution of these groups to nitrogenase transcription was disproportionately high. CONCLUSIONS The substantial variation in community structure among active dizatrophic fractions compared to the total communities suggests that the former are better indicators of biological response to environmental changes. Altogether, our study highlights the importance of rare PADs groups in nitrogen fixation in plankton holobionts, evidenced by their high level of nitrogenase transcription.
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Affiliation(s)
- Qing-Song Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-De Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Manzoor Ahmad
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Wei-Guo Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye-Hui Tan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yuan-Zhou Zhang
- State Oceanic Administration Sansha Marine Environmental Monitoring Center Station, Haikou, 570311, China
| | - Dan-Dan Shen
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, 18119, Warnemünde, Germany.
| | - Yan-Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China.
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Zhou W, Zhu P, Qu W. Basic Properties of Calcined Underground Ant Nest Materials and Its Influence on the Compressive Strength of Concrete. MATERIALS (BASEL, SWITZERLAND) 2019; 12:ma12071191. [PMID: 30979039 PMCID: PMC6480646 DOI: 10.3390/ma12071191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 06/02/2023]
Abstract
Underground ant nests are typically made of soil and rubble mixed with dead plant bodies, ant secretions, and other organic substances. The clay content is high, and the natural clay materials show pozzolanic activity after calcination. In this study, the underground ant nest materials of Iridomyrmex anceps, which is a common ant in the Shanghai area, are calcined and ground, and the material properties of calcined ant nest clay powder (CANCP) are characterized from six aspects: chemical composition, particle morphology, specific gravity, specific surface area, particle size distribution and pozzolanic activity index. The pozzolanic activity of CANCP is evaluated by the strength contribution rate of pozzolanic activity, revealing that CANCP is beneficial to the strength of the mortar system from an early age. The influence of CANCP on the compressive strength of concrete is analyzed using three aspects, namely, content, curing age and calcination temperature, and it is found that the three aspects of CANCP have a strong influence on the compressive strength of concrete.
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Affiliation(s)
- Wei Zhou
- Department of Structural Engineering, Tongji University, Shanghai 200092, China.
| | - Peng Zhu
- Department of Structural Engineering, Tongji University, Shanghai 200092, China.
| | - Wenjun Qu
- Department of Structural Engineering, Tongji University, Shanghai 200092, China.
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Bolaños LM, Rosenblueth M, Manrique de Lara A, Migueles-Lozano A, Gil-Aguillón C, Mateo-Estrada V, González-Serrano F, Santibáñez-López CE, García-Santibáñez T, Martínez-Romero E. Cophylogenetic analysis suggests cospeciation between the Scorpion Mycoplasma Clade symbionts and their hosts. PLoS One 2019; 14:e0209588. [PMID: 30625167 PMCID: PMC6326461 DOI: 10.1371/journal.pone.0209588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/08/2018] [Indexed: 11/19/2022] Open
Abstract
Scorpions are predator arachnids of ancient origin and worldwide distribution. Two scorpion species, Vaejovis smithi and Centruroides limpidus, were found to harbor two different Mollicutes phylotypes: a Scorpion Mycoplasma Clade (SMC) and Scorpion Group 1 (SG1). Here we investigated, using a targeted gene sequencing strategy, whether these Mollicutes were present in 23 scorpion morphospecies belonging to the Vaejovidae, Carboctonidae, Euscorpiidae, Diplocentridae, and Buthidae families. Our results revealed that SMC is found in a species-specific association with Vaejovidae and Buthidae, whereas SG1 is uniquely found in Vaejovidae. SMC and SG1 co-occur only in Vaejovis smithi where 43% of the individuals host both phylotypes. A phylogenetic analysis of Mollicutes 16S rRNA showed that SMC and SG1 constitute well-delineated phylotypes. Additionally, we found that SMC and scorpion phylogenies are significantly congruent, supporting the observation that a cospeciation process may have occurred. This study highlights the phylogenetic diversity of the scorpion associated Mollicutes through different species revealing a possible cospeciation pattern.
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Affiliation(s)
- Luis M. Bolaños
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Mónica Rosenblueth
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Amaranta Manrique de Lara
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Analí Migueles-Lozano
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Citlali Gil-Aguillón
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Valeria Mateo-Estrada
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Francisco González-Serrano
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Carlos E. Santibáñez-López
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Tonalli García-Santibáñez
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Esperanza Martínez-Romero
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
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Reese AT, Pereira FC, Schintlmeister A, Berry D, Wagner M, Hale LP, Wu A, Jiang S, Durand HK, Zhou X, Premont RT, Diehl AM, O'Connell TM, Alberts SC, Kartzinel TR, Pringle RM, Dunn RR, Wright JP, David LA. Microbial nitrogen limitation in the mammalian large intestine. Nat Microbiol 2018; 3:1441-1450. [PMID: 30374168 PMCID: PMC6264799 DOI: 10.1038/s41564-018-0267-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023]
Abstract
Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.
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Affiliation(s)
- Aspen T Reese
- Department of Biology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Fátima C Pereira
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - David Berry
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Laura P Hale
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Anchi Wu
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Heather K Durand
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Xiyou Zhou
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Richard T Premont
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Anna Mae Diehl
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Thomas M O'Connell
- Department of Otolaryngology - Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Tyler R Kartzinel
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Robert M Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | | | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
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Ikeda-Ohtsubo W, Brugman S, Warden CH, Rebel JMJ, Folkerts G, Pieterse CMJ. How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture. Front Nutr 2018; 5:90. [PMID: 30333981 PMCID: PMC6176000 DOI: 10.3389/fnut.2018.00090] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/07/2018] [Indexed: 12/21/2022] Open
Abstract
All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.
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Affiliation(s)
- Wakako Ikeda-Ohtsubo
- Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Sylvia Brugman
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
| | - Craig H Warden
- Departments of Pediatrics, Neurobiology Physiology and Behavior, University of California, Davis, Davis, CA, United States
| | - Johanna M J Rebel
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Gert Folkerts
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
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Terry SA, Ribeiro GDO, Gruninger RJ, Hunerberg M, Ping S, Chaves AV, Burlet J, Beauchemin KA, McAllister TA. Effect of humic substances on rumen fermentation, nutrient digestibility, methane emissions, and rumen microbiota in beef heifers1. J Anim Sci 2018; 96:3863-3877. [PMID: 30169754 PMCID: PMC6127782 DOI: 10.1093/jas/sky265] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/05/2018] [Indexed: 11/13/2022] Open
Abstract
Ruminants play an important role in food security, but there is a growing concern about the impact of cattle on the environment, particularly regarding greenhouse gas emissions. The objective of this study was to examine the effect of humic substances (HS) on rumen fermentation, nutrient digestibility, methane (CH4) emissions, and the rumen microbiome of beef heifers fed a barley silage-based diet. The experiment was designed as a replicated 4 × 4 Latin square using 8 ruminally cannulated Angus × Hereford heifers (758 ± 40.7 kg initial BW). Heifers were offered a basal diet consisting of 60% barley silage and 40% concentrate (DM basis) with either 0- (control), 100-, 200- or 300-mg granulated HS/kg BW. Each period was 28 d with 14 d of adaptation. Rumen samples were taken on day 15 at 0, 3, 6, and 12 h postfeeding. Total urine and feces were collected from days 18 to 22. Blood samples were taken on day 22 at 0 and 6 h postfeeding. Between days 26 and 28, heifers were placed in open-circuit respiratory chambers to measure CH4. Ruminal pH was recorded continuously during the periods of CH4 measurement using indwelling pH loggers. Intake was similar (P = 0.47) across treatments. Concentration of ammonia-N and counts of rumen protozoa responded quadratically (P = 0.03), where both increased at H100 and then decreased for the H300 treatments. Apparent total tract digestibility of CP (P = 0.04) was linearly increased by HS and total N retention (g/d, % N intake, g/kg BW0.75) was improved (P = 0.04) for HS when compared with the control. There was no effect of HS on CH4 production (g/d; P = 0.83); however, HS decreased the relative abundance of Proteobacteria (P = 0.04) and increased the relative abundance of Synergistetes (P = 0.01) and Euryarchaeota (P = 0.04). Results suggest that HS included at up to 300 mg/kg BW may improve N retention and CP digestibility, but there was no impact on CH4 production.
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Affiliation(s)
- Stephanie A Terry
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Gabriel de Oliveira Ribeiro
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- University of Calgary, Department of Production Animal Health, Calgary, Alberta, Canada
| | - Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Martin Hunerberg
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- University of Goettingen, Department of Animal Sciences, Goettingen, Germany
| | - Sheng Ping
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, China
| | - Alex V Chaves
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
| | - Jake Burlet
- Venture West Veterinary Services Ltd, Edmonton, Alberta, Canada
| | - Karen Ann Beauchemin
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Tim Angus McAllister
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
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Gao G, Gao J, Hao C, Dai L, Chen H. Biodiversity and Activity of Gut Fungal Communities across the Life History of Trypophloeus klimeschi (Coleoptera: Curculionidae: Scolytinae). Int J Mol Sci 2018; 19:ijms19072010. [PMID: 29996485 PMCID: PMC6073459 DOI: 10.3390/ijms19072010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/27/2018] [Accepted: 07/05/2018] [Indexed: 02/07/2023] Open
Abstract
We comprehensively investigated the biodiversity of fungal communities in different developmental stages of Trypophloeus klimeschi and the difference between sexes and two generations by high throughput sequencing. The predominant species found in the intestinal fungal communities mainly belong to the phyla Ascomycota and Basidiomycota. Fungal community structure varies with life stage. The genera Nakazawaea, Trichothecium, Aspergillus, Didymella, Villophora, and Auricularia are most prevalent in the larvae samples. Adults harbored high proportions of Graphium. The fungal community structures found in different sexes are similar. Fusarium is the most abundant genus and conserved in all development stages. Gut fungal communities showed notable variation in relative abundance during the overwintering stage. Fusarium and Nectriaceae were significantly increased in overwintering mature larvae. The data indicates that Fusarium might play important roles in the survival of T. klimeschi especially in the overwintering stage. The authors speculated that Graphium plays an important role in the invasion and colonization of T. klimeschi. The study will contribute to the understanding of the biological role of the intestinal fungi in T. klimeschi, which might provide an opportunity and theoretical basis to promote integrated pest management (IPM) of T. klimeschi.
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Affiliation(s)
- Guanqun Gao
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Jing Gao
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Chunfeng Hao
- Tianjin Forestry Pest Control and Quarantine Station, Tianjin 300000, China.
| | - Lulu Dai
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Hui Chen
- College of Forestry, Northwest A&F University, Yangling 712100, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.
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van de Water JAJM, Allemand D, Ferrier-Pagès C. Host-microbe interactions in octocoral holobionts - recent advances and perspectives. MICROBIOME 2018; 6:64. [PMID: 29609655 PMCID: PMC5880021 DOI: 10.1186/s40168-018-0431-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/01/2018] [Indexed: 05/05/2023]
Abstract
Octocorals are one of the most ubiquitous benthic organisms in marine ecosystems from the shallow tropics to the Antarctic deep sea, providing habitat for numerous organisms as well as ecosystem services for humans. In contrast to the holobionts of reef-building scleractinian corals, the holobionts of octocorals have received relatively little attention, despite the devastating effects of disease outbreaks on many populations. Recent advances have shown that octocorals possess remarkably stable bacterial communities on geographical and temporal scales as well as under environmental stress. This may be the result of their high capacity to regulate their microbiome through the production of antimicrobial and quorum-sensing interfering compounds. Despite decades of research relating to octocoral-microbe interactions, a synthesis of this expanding field has not been conducted to date. We therefore provide an urgently needed review on our current knowledge about octocoral holobionts. Specifically, we briefly introduce the ecological role of octocorals and the concept of holobiont before providing detailed overviews of (I) the symbiosis between octocorals and the algal symbiont Symbiodinium; (II) the main fungal, viral, and bacterial taxa associated with octocorals; (III) the dominance of the microbial assemblages by a few microbial species, the stability of these associations, and their evolutionary history with the host organism; (IV) octocoral diseases; (V) how octocorals use their immune system to fight pathogens; (VI) microbiome regulation by the octocoral and its associated microbes; and (VII) the discovery of natural products with microbiome regulatory activities. Finally, we present our perspectives on how the field of octocoral research should move forward, and the recognition that these organisms may be suitable model organisms to study coral-microbe symbioses.
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Affiliation(s)
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
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Provorov NA, Onishchuk OP. Microbial Symbionts of Insects: Genetic Organization, Adaptive Role, and Evolution. Microbiology (Reading) 2018. [DOI: 10.1134/s002626171802011x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Nutrient Dynamics in Decomposing Dead Wood in the Context of Wood Eater Requirements: The Ecological Stoichiometry of Saproxylophagous Insects. SAPROXYLIC INSECTS 2018. [DOI: 10.1007/978-3-319-75937-1_13] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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van de Water JAJM, Voolstra CR, Rottier C, Cocito S, Peirano A, Allemand D, Ferrier-Pagès C. Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea. MICROBIAL ECOLOGY 2018; 75:274-288. [PMID: 28681143 DOI: 10.1007/s00248-017-1006-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/02/2017] [Indexed: 06/07/2023]
Abstract
Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same 'core microbiome' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of 'core' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.
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Affiliation(s)
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Cecile Rottier
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
| | - Silvia Cocito
- Marine Environment Research Centre, ENEA, La Spezia, Italy
| | - Andrea Peirano
- Marine Environment Research Centre, ENEA, La Spezia, Italy
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, Monaco
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