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Marulanda-Gomez AM, Ribes M, Franzenburg S, Hentschel U, Pita L. Transcriptomic responses of Mediterranean sponges upon encounter with symbiont microbial consortia. BMC Genomics 2024; 25:674. [PMID: 38972970 PMCID: PMC11229196 DOI: 10.1186/s12864-024-10548-z] [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: 03/06/2024] [Accepted: 06/21/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Sponges (phylum Porifera) constantly interact with microbes. They graze on microbes from the water column by filter-feeding and they harbor symbiotic partners within their bodies. In experimental setups, sponges take up symbionts at lower rates compared with seawater microbes. This suggests that sponges have the capacity to differentiate between microbes and preferentially graze in non-symbiotic microbes, although the underlying mechanisms of discrimination are still poorly understood. Genomic studies showed that, compared to other animal groups, sponges present an extended repertoire of immune receptors, in particular NLRs, SRCRs, and GPCRs, and a handful of experiments showed that sponges regulate the expression of these receptors upon encounter with microbial elicitors. We hypothesize that sponges may rely on differential expression of their diverse repertoire of poriferan immune receptors to sense different microbial consortia while filter-feeding. To test this, we characterized the transcriptomic response of two sponge species, Aplysina aerophoba and Dysidea avara, upon incubation with microbial consortia extracted from A. aerophoba in comparison with incubation with seawater microbes. The sponges were sampled after 1 h, 3 h, and 5 h for RNA-Seq differential gene expression analysis. RESULTS D. avara incubated with A. aerophoba-symbionts regulated the expression of genes related to immunity, ubiquitination, and signaling. Within the set of differentially-expressed immune genes we identified different families of Nucleotide Oligomerization Domain (NOD)-Like Receptors (NLRs). These results represent the first experimental evidence that different types of NLRs are involved in microbial discrimination in a sponge. In contrast, the transcriptomic response of A. aerophoba to its own symbionts involved comparatively fewer genes and lacked genes encoding for immune receptors. CONCLUSION Our work suggests that: (i) the transcriptomic response of sponges upon microbial exposure may imply "fine-tuning" of baseline gene expression as a result of their interaction with microbes, (ii) the differential response of sponges to microbial encounters varied between the species, probably due to species-specific characteristics or related to host's traits, and (iii) immune receptors belonging to different families of NLR-like genes played a role in the differential response to microbes, whether symbionts or food bacteria. The regulation of these receptors in sponges provides further evidence of the potential role of NLRs in invertebrate host-microbe interactions. The study of sponge responses to microbes exemplifies how investigating different animal groups broadens our knowledge of the evolution of immune specificity and symbiosis.
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Affiliation(s)
| | - Marta Ribes
- Institut de Ciències del Mar, ICM - CSIC, Barcelona, Spain
| | - Sören Franzenburg
- Research Group Genetics and Bioinformatics/Systems Immunology, Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Ute Hentschel
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Lucia Pita
- Institut de Ciències del Mar, ICM - CSIC, Barcelona, Spain.
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2
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Neubauer A, Aros-Mualin D, Mariscal V, Szövényi P. Challenging the term symbiosis in plant-microbe associations to create an understanding across sciences. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:7-11. [PMID: 38038369 DOI: 10.1111/jipb.13588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Scientific progress relies on clear and consistent definitions for effective communication and collaboration. The term "symbiosis" in the context of plant-microbe associations suffers from diverse interpretations, leading to ambiguity in classification of these associations. This review elaborates on the issue, proposing an inclusive definition as well as a keyword.
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Affiliation(s)
- Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
- Zurich-Basel Plant Science Center, Zurich, 8092, Switzerland
| | - Daniela Aros-Mualin
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Vicente Mariscal
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC y Universidad de Sevilla, Sevilla, 41092, Spain
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
- Zurich-Basel Plant Science Center, Zurich, 8092, Switzerland
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3
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Guo Y, Meng L, Wang M, Zhong Z, Li D, Zhang Y, Li H, Zhang H, Seim I, Li Y, Jiang A, Ji Q, Su X, Chen J, Fan G, Li C, Liu S. Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves. BMC Biol 2023; 21:51. [PMID: 36882766 PMCID: PMC9993606 DOI: 10.1186/s12915-023-01551-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Bivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves. Here, we investigate the hologenome of an extracellular symbiotic thyasirid clam that represents the early stages of symbiosis evolution. RESULTS We present a hologenome of Conchocele bisecta (Bivalvia: Thyasiridae) collected from deep-sea hydrothermal vents with extracellular symbionts, along with related ultrastructural evidence and expression data. Based on ultrastructural and sequencing evidence, only one dominant Thioglobaceae bacteria was densely aggregated in the large bacterial chambers of C. bisecta, and the bacterial genome shows nutritional complementarity and immune interactions with the host. Overall, gene family expansions may contribute to the symbiosis-related phenotypic variations in different bivalves. For instance, convergent expansions of gaseous substrate transport families in the endosymbiotic bivalves are absent in C. bisecta. Compared to endosymbiotic relatives, the thyasirid genome exhibits large-scale expansion in phagocytosis, which may facilitate symbiont digestion and account for extracellular symbiotic phenotypes. We also reveal that distinct immune system evolution, including expansion in lipopolysaccharide scavenging and contraction of IAP (inhibitor of apoptosis protein), may contribute to the different manners of bacterial virulence resistance in C. bisecta. CONCLUSIONS Thus, bivalves employ different pathways to adapt to the long-term co-existence with their bacterial symbionts, further highlighting the contribution of stochastic evolution to the independent gain of a symbiotic lifestyle in the lineage.
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Affiliation(s)
- Yang Guo
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lingfeng Meng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minxiao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Denghui Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Hanbo Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China.,School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Yuli Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Aijun Jiang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Qianyue Ji
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Xiaoshan Su
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. .,BGI-Shenzhen, Shenzhen, 518083, China.
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,College of Marine Science, University of Chinese Academy of Sciences, Qingdao, 266400, China. .,South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. .,Qingdao Key Laboratory of Marine Genomics, BGI-qingdao, Qingdao, China.
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4
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Maor-Landaw K, Eisenhut M, Tortorelli G, van de Meene A, Kurz S, Segal G, van Oppen MJH, Weber APM, McFadden GI. A candidate transporter allowing symbiotic dinoflagellates to feed their coral hosts. ISME COMMUNICATIONS 2023; 3:7. [PMID: 36709382 PMCID: PMC9884229 DOI: 10.1038/s43705-023-00218-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 01/30/2023]
Abstract
The symbiotic partnership between corals and dinoflagellate algae is crucial to coral reefs. Corals provide their algal symbionts with shelter, carbon dioxide and nitrogen. In exchange, the symbiotic algae supply their animal hosts with fixed carbon in the form of glucose. But how glucose is transferred from the algal symbiont to the animal host is unknown. We reasoned that a transporter resident in the dinoflagellate cell membrane would facilitate outward transfer of glucose to the surrounding host animal tissue. We identified a candidate transporter in the cnidarian symbiont dinoflagellate Breviolum minutum that belongs to the ubiquitous family of facilitative sugar uniporters known as SWEETs (sugars will eventually be exported transporters). Previous gene expression analyses had shown that BmSWEET1 is upregulated when the algae are living symbiotically in a cnidarian host by comparison to the free-living state [1, 2]. We used immunofluorescence microscopy to localise BmSWEET1 in the dinoflagellate cell membrane. Substrate preference assays in a yeast surrogate transport system showed that BmSWEET1 transports glucose. Quantitative microscopy showed that symbiotic B. minutum cells have significantly more BmSWEET1 protein than free-living cells of the same strain, consistent with export during symbiosis but not during the free-living, planktonic phase. Thus, BmSWEET1 is in the right place, at the right time, and has the right substrate to be the transporter with which symbiotic dinoflagellate algae feed their animal hosts to power coral reefs.
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Affiliation(s)
- Keren Maor-Landaw
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Marion Eisenhut
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Giada Tortorelli
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
- Coral Resilience Lab, Hawai'i Institute of Marine Biology, Kāne'ohe, HI, USA
| | | | - Samantha Kurz
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
| | - Gabriela Segal
- Biological Optical Microscopy Platform, The University of Melbourne, Parkville, VIC, Australia
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
| | - Geoffrey I McFadden
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia.
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5
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The Microbiome of the Built Environment: The Nexus for Urban Regeneration for the Cities of Tomorrow. Microorganisms 2022; 10:microorganisms10122311. [PMID: 36557564 PMCID: PMC9783557 DOI: 10.3390/microorganisms10122311] [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] [Received: 10/17/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Built environments are, for most of us, our natural habitat. In the last 50 years, the built-up area has more than doubled, with a massive biodiversity loss. The undeniable benefits of a city providing all the basic needs to a growing population showed longer-term and less obvious costs to human health: autoimmune and non-communicable diseases, as well as antimicrobial resistance, have reached unprecedented and alarming levels. Humans coevolved with microbes, and this long-lasting alliance is affected by the loss of connection with natural environments, misuse of antibiotics, and highly sanitized environments. Our aim is to direct the focus onto the microbial communities harbored by the built environments we live in. They represent the nexus for urban regeneration, which starts from a healthy environment. Planning a city means considering, in a two-fold way, the ecosystem health and the multidimensional aspects of wellbeing, including social, cultural, and aesthetic values. The significance of this perspective is inspiring guidelines and strategies for the urban regeneration of the cities of tomorrow, exploiting the invaluable role of microbial biodiversity and the ecosystem services that it could provide to create the robust scientific knowledge that is necessary for a bioinformed design of buildings and cities for healthy and sustainable living.
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6
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Zakalyukina YV, Pavlov NA, Lukianov DA, Marina VI, Belozerova OA, Tashlitsky VN, Guglya EB, Osterman IA, Biryukov MV. A New Albomycin-Producing Strain of Streptomyces globisporus subsp. globisporus May Provide Protection for Ants Messor structor. INSECTS 2022; 13:1042. [PMID: 36421945 PMCID: PMC9693239 DOI: 10.3390/insects13111042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
There are several well-studied examples of protective symbiosis between insect host and symbiotic actinobacteria, producing antimicrobial metabolites to inhibit host pathogens. These mutualistic relationships are best described for some wasps and leaf-cutting ants, while a huge variety of insect species still remain poorly explored. For the first time, we isolated actinobacteria from the harvester ant Messor structor and evaluated the isolates' potential as antimicrobial producers. All isolates could be divided into two morphotypes of single and mycelial cells. We found that the most common mycelial morphotype was observed among soldiers and least common among larvae in the studied laboratory colony. The representative of this morphotype was identified as Streptomyces globisporus subsp. globisporus 4-3 by a polyphasic approach. It was established using a E. coli JW5503 pDualRep2 system that crude broths of mycelial isolates inhibited protein synthesis in reporter strains, but it did not disrupt the in vitro synthesis of proteins in cell-free extracts. An active compound was extracted, purified and identified as albomycin δ2. The pronounced ability of albomycin to inhibit the growth of entomopathogens suggests that Streptomyces globisporus subsp. globisporus may be involved in defensive symbiosis with the Messor structor ant against infections.
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Affiliation(s)
- Yuliya V. Zakalyukina
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Department of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Nikolay A. Pavlov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Valeria I. Marina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russia
| | - Vadim N. Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Elena B. Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova st. 1, 117997 Moscow, Russia
| | - Ilya A. Osterman
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Mikhail V. Biryukov
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
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7
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Lee H, Park J, Kim N, Youn W, Yun G, Han SY, Nguyen DT, Choi IS. Cell-in-Catalytic-Shell Nanoarchitectonics: Catalytic Empowerment of Individual Living Cells by Single-Cell Nanoencapsulation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2201247. [PMID: 35641454 DOI: 10.1002/adma.202201247] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Cell-in-shell biohybrid structures, synthesized by encapsulating individual living cells with exogenous materials, have emerged as exciting functional entities for engineered living materials, with emergent properties outside the scope of biochemical modifications. Artificial exoskeletons have, to date, provided physicochemical shelters to the cells inside in the first stage of technological development, and further advances in the field demand catalytically empowered, cellular hybrid systems that augment the biological functions of cells and even introduce completely new functions to the cells. This work describes a facile and generalizable strategy for empowering living cells with extrinsic catalytic capability through nanoencapsulation of living cells with a supramolecular metal-organic complex of Fe3+ and benzene-1,3,5-tricarboxylic acid (BTC). A series of enzymes are embedded in situ, without loss of catalytic activity, in the Fe3+ -BTC shells, not to mention the superior characteristics of cytocompatible and rapid shell-forming processes. The nanoshell enhances the catalytic efficiency of multienzymatic cascade reactions by confining reaction intermediates to its internal voids and the nanoencapsulated cells acquire exogenous biochemical functions, including enzymatic cleavage of lethal octyl-β-d-glucopyranoside into d-glucose, with autonomous cytoprotection. The system will provide a versatile, nanoarchitectonic tool for interfacing biological cells with functional materials, especially for catalytic bioempowerment of living cells.
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Affiliation(s)
- Hojae Lee
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon, 34141, South Korea
| | - Joohyouck Park
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon, 34141, South Korea
| | - Nayoung Kim
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon, 34141, South Korea
| | - Wongu Youn
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon, 34141, South Korea
| | - Gyeongwon Yun
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon, 34141, South Korea
| | - Sang Yeong Han
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon, 34141, South Korea
| | - Duc Tai Nguyen
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon, 34141, South Korea
| | - Insung S Choi
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon, 34141, South Korea
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8
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Woehle C, Roy AS, Glock N, Michels J, Wein T, Weissenbach J, Romero D, Hiebenthal C, Gorb SN, Schönfeld J, Dagan T. Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria. Proc Natl Acad Sci U S A 2022; 119:e2200198119. [PMID: 35704763 PMCID: PMC9231491 DOI: 10.1073/pnas.2200198119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.
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Affiliation(s)
- Christian Woehle
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
| | | | - Nicolaas Glock
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24148, Germany
| | - Jan Michels
- Zoological Institute, Kiel University, Kiel 24118, Germany
| | - Tanita Wein
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
| | - Julia Weissenbach
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
| | - Dennis Romero
- Dirección General de Investigaciones Oceanográficas y Cambio Climático, Instituto del Mar del Perú, Callao 01, Peru 17
| | - Claas Hiebenthal
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24148, Germany
| | | | - Joachim Schönfeld
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24148, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel 24118, Germany
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9
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Pineda-Mendoza RM, Zúñiga G, López MF, Hidalgo-Lara ME, Santiago-Hernández A, López-López A, Orduña FNR, Cano-Ramírez C. Rahnella sp., a Dominant Symbiont of the Core Gut Bacteriome of Dendroctonus Species, Has Metabolic Capacity to Degrade Xylan by Bifunctional Xylanase-Ferulic Acid Esterase. Front Microbiol 2022; 13:911269. [PMID: 35711755 PMCID: PMC9195170 DOI: 10.3389/fmicb.2022.911269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Rahnella sp. ChDrAdgB13 is a dominant member of the gut bacterial core of species of the genus Dendroctonus, which is one of the most destructive pine forest bark beetles. The objectives of this study were identified in Rahnella sp. ChDrAdgB13 genome the glycosyl hydrolase families involved in carbohydrate metabolism and specifically, the genes that participate in xylan hydrolysis, to determine the functionality of a putative endo-1,4-β-D-xylanase, which results to be bifunctional xylanase-ferulic acid esterase called R13 Fae and characterize it biochemically. The carbohydrate-active enzyme prediction revealed 25 glycoside hydrolases, 20 glycosyl transferases, carbohydrate esterases, two auxiliary activities, one polysaccharide lyase, and one carbohydrate-binding module (CBM). The R13 Fae predicted showed high identity to the putative esterases and glycosyl hydrolases from Rahnella species and some members of the Yersiniaceae family. The r13 fae gene encodes 393 amino acids (43.5 kDa), containing a signal peptide, esterase catalytic domain, and CBM48. The R13 Fae modeling showed a higher binding affinity to ferulic acid, α-naphthyl acetate, and arabinoxylan, and a low affinity to starch. The R13 Fae recombinant protein showed activity on α-naphthyl acetate and xylan, but not on starch. This enzyme showed mesophilic characteristics, displaying its optimal activity at pH 6.0 and 25°C. The enzyme was stable at pH from 4.5 to 9.0, retaining nearly 66-71% of its original activity. The half-life of the enzyme was 23 days at 25°C. The enzyme was stable in the presence of metallic ions, except for Hg2+. The products of R13 Fae mediated hydrolysis of beechwood xylan were xylobiose and xylose, manifesting an exo-activity. The results suggest that Rahnella sp. ChDrAdgB13 hydrolyze xylan and its products could be assimilated by its host and other gut microbes as a nutritional source, demonstrating their functional role in the bacterial-insect interaction contributing to their fitness, development, and survival.
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Affiliation(s)
- Rosa María Pineda-Mendoza
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Gerardo Zúñiga
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - María Fernanda López
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - María Eugenia Hidalgo-Lara
- Laboratorio de Ingeniería de Proteínas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Biotecnología y Bioingeniería, Mexico City, Mexico
| | - Alejandro Santiago-Hernández
- Laboratorio de Ingeniería de Proteínas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Biotecnología y Bioingeniería, Mexico City, Mexico
| | - Azucena López-López
- Laboratorio de Ingeniería de Proteínas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Biotecnología y Bioingeniería, Mexico City, Mexico
| | - Flor N. Rivera Orduña
- Laboratorio de Ecología Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Claudia Cano-Ramírez
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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10
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Wang Y, Xie Y, Qi L, He Y, Bo H. Synergies evaluation and influencing factors analysis of the water-energy-food nexus from symbiosis perspective: A case study in the Beijing-Tianjin-Hebei region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151731. [PMID: 34800449 DOI: 10.1016/j.scitotenv.2021.151731] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/23/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
In the context of global population growth and environmental degradation, research on the synergies of the water-energy-food (WEF) nexus is important for sustainable regional development. Using symbiosis and synergy theories, the authors constructed a synergy evaluation index for the WEF nexus and used the set pair analysis-variable fuzzy sets model to analyze the WEF nexus synergies in the Beijing-Tianjin-Hebei region (BTH) of China, from 2005 to 2017. The main factors affecting WEF nexus synergies were also analyzed, with results indicating that: 1) the WEF nexus synergies were the best in Beijing, followed by the BTH as a whole, Tianjin, and then Hebei. We also found that WEF nexus synergy grades have been gradually improving over time, with Beijing improving the most, and Tianjin the least. 2) The WEF nexus synergy grades in each region, for symbiotic units, symbiotic relationships, and symbiotic environments, have also gradually improved. And symbiotic relationship synergies were better than symbiotic environment synergies than symbiotic unit synergies. 3) The WEF nexus symbiotic unit synergies were strongest in Tianjin, followed by Beijing, the BTH as a whole, and then Hebei. The symbiotic relationship synergies were strongest in Beijing, followed by Hebei, the BTH as a whole, and then Tianjin. The symbiotic environment synergies were also strongest in Beijing, followed this time by the BTH as a whole, Tianjin, and then Hebei. 4) Economic factors and symbiotic unit synergies were found to be the aspects most influential on WEF nexus synergies in each region. In addition, symbiotic relationship synergies were found to have important impacts on the WEF nexus synergies in Hebei and the BTH as a whole. Overall, we were able to conclude that the methodology developed in this study provided a scientific basis for synergy optimization in the context of a regional WEF nexus.
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Affiliation(s)
- Yong Wang
- School of Statistics, Dongbei University of Finance and Economics, Dalian 116025, China.
| | - Yanjing Xie
- School of Statistics, Dongbei University of Finance and Economics, Dalian 116025, China.
| | - Lin Qi
- School of Statistics, Dongbei University of Finance and Economics, Dalian 116025, China.
| | - Yuan He
- School of Finance, Dongbei University of Financial and Economics, Dalian 116025, China.
| | - He Bo
- School of Economics, Dongbei University of Finance and Economics, Dalian 116025, China.
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11
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Solomon R, Wein T, Levy B, Eshed S, Dror R, Reiss V, Zehavi T, Furman O, Mizrahi I, Jami E. Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem. THE ISME JOURNAL 2022; 16:1187-1197. [PMID: 34887549 PMCID: PMC8941083 DOI: 10.1038/s41396-021-01170-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023]
Abstract
Unicellular eukaryotes are an integral part of many microbial ecosystems where they interact with their surrounding prokaryotic community-either as predators or as mutualists. Within the rumen, one of the most complex host-associated microbial habitats, ciliate protozoa represent the main micro-eukaryotes, accounting for up to 50% of the microbial biomass. Nonetheless, the extent of the ecological effect of protozoa on the microbial community and on the rumen metabolic output remains largely understudied. To assess the role of protozoa on the rumen ecosystem, we established an in-vitro system in which distinct protozoa sub-communities were introduced to the native rumen prokaryotic community. We show that the different protozoa communities exert a strong and differential impact on the composition of the prokaryotic community, as well as its function including methane production. Furthermore, the presence of protozoa increases prokaryotic diversity with a differential effect on specific bacterial populations such as Gammaproteobacteria, Prevotella and Treponema. Our results suggest that protozoa contribute to the maintenance of prokaryotic diversity in the rumen possibly by mitigating the effect of competitive exclusion between bacterial taxa. Our findings put forward the rumen protozoa populations as potentially important ecosystem engineers for future microbiome modulation strategies.
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Affiliation(s)
- Ronnie Solomon
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel ,grid.7489.20000 0004 1937 0511Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Tanita Wein
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Bar Levy
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel ,grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shahar Eshed
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Rotem Dror
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Veronica Reiss
- grid.410498.00000 0001 0465 9329Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Tamar Zehavi
- grid.7489.20000 0004 1937 0511Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Ori Furman
- grid.7489.20000 0004 1937 0511Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Itzhak Mizrahi
- grid.7489.20000 0004 1937 0511Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Elie Jami
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel.
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12
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Abstract
Can hosts swap ancient symbionts for new ones? A new study shows that a novel partnership between a protist and an algal symbiont can rapidly evolve to both overcome initial incompatibility and adapt to environmental challenges.
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Affiliation(s)
- Stephanie Porter
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA.
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13
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Abstract
Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and "farmed" organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.
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Affiliation(s)
- Erik F. Y. Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS 38677 USA
| | - Alexandra S. Penn
- Department of Sociology and Centre for Evaluation of Complexity Across the Nexus, University of Surrey, Guildford, Surrey, GU2 7XH UK
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14
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Zhang J, Luo W, Wang Z, Chen X, Lv P, Xu J. A novel strategy for D-psicose and lipase co-production using a co-culture system of engineered Bacillus subtilis and Escherichia coli and bioprocess analysis using metabolomics. BIORESOUR BIOPROCESS 2021; 8:77. [PMID: 38650263 PMCID: PMC10992840 DOI: 10.1186/s40643-021-00429-8] [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: 05/17/2021] [Accepted: 08/11/2021] [Indexed: 11/10/2022] Open
Abstract
To develop an economically feasible fermentation process, this study designed a novel bioprocess based on the co-culture of engineered Bacillus subtilis and Escherichia coli for the co-production of extracellular D-psicose and intracellular lipase. After optimizing the co-culture bioprocess, 11.70 g/L of D-psicose along with 16.03 U/mg of lipase was obtained; the glucose and fructose were completely utilized. Hence, the conversion rate of D-psicose reached 69.54%. Compared with mono-culture, lipase activity increased by 58.24%, and D-psicose production increased by 7.08%. In addition, the co-culture bioprocess was explored through metabolomics analysis, which included 168 carboxylic acids and derivatives, 70 organooxygen compounds, 34 diazines, 32 pyridines and derivatives, 30 benzene and substituted derivatives, and other compounds. It also could be found that the relative abundance of differential metabolites in the co-culture system was significantly higher than that in the mono-culture system. Pathway analysis revealed that, tryptophan metabolism and β-alanine metabolism had the highest correlation and played an important role in the co-culture system; among them, tryptophan metabolism regulates protein synthesis and β-alanine metabolism, which is related to the formation of metabolic by-products. These results confirm that the co-cultivation of B. subtilis and E. coli can provide a novel idea for D-psicose and lipase biorefinery, and are beneficial for the discovery of valuable secondary metabolites such as turanose and morusin.
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Affiliation(s)
- Jun Zhang
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, 524088 , China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen Luo
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
| | - Zhiyuan Wang
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
| | - Xiaoyan Chen
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengmei Lv
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China.
| | - Jingliang Xu
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China.
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001 , China.
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15
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Li E, de Jonge R, Liu C, Jiang H, Friman VP, Pieterse CMJ, Bakker PAHM, Jousset A. Rapid evolution of bacterial mutualism in the plant rhizosphere. Nat Commun 2021; 12:3829. [PMID: 34158504 PMCID: PMC8219802 DOI: 10.1038/s41467-021-24005-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.
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Affiliation(s)
- Erqin Li
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands ,grid.14095.390000 0000 9116 4836Freie Universität Berlin, Institut für Biologie, Berlin, Germany ,grid.452299.1Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Ronnie de Jonge
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands ,grid.11486.3a0000000104788040VIB Center for Plant Systems Biology, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
| | - Chen Liu
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Henan Jiang
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Ville-Petri Friman
- grid.5685.e0000 0004 1936 9668University of York, Department of Biology, York, UK
| | - Corné M. J. Pieterse
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Peter A. H. M. Bakker
- grid.5477.10000000120346234Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Alexandre Jousset
- grid.5477.10000000120346234Utrecht University, Department of Biology, Ecology and Biodiversity, Utrecht, The Netherlands
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16
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Li E, de Jonge R, Liu C, Jiang H, Friman VP, Pieterse CMJ, Bakker PAHM, Jousset A. Rapid evolution of bacterial mutualism in the plant rhizosphere. Nat Commun 2021. [PMID: 34158504 DOI: 10.1038/s41467-012-24005-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.
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Affiliation(s)
- Erqin Li
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Ronnie de Jonge
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
| | - Chen Liu
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Henan Jiang
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | | | - Corné M J Pieterse
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Peter A H M Bakker
- Utrecht University, Department of Biology, Plant-Microbe Interactions, Utrecht, The Netherlands
| | - Alexandre Jousset
- Utrecht University, Department of Biology, Ecology and Biodiversity, Utrecht, The Netherlands.
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17
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Collens AB, Katz LA. Opinion: Genetic Conflict With Mobile Elements Drives Eukaryotic Genome Evolution, and Perhaps Also Eukaryogenesis. J Hered 2021; 112:140-144. [PMID: 33538295 PMCID: PMC7953837 DOI: 10.1093/jhered/esaa060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Through analyses of diverse microeukaryotes, we have previously argued that eukaryotic genomes are dynamic systems that rely on epigenetic mechanisms to distinguish germline (i.e., DNA to be inherited) from soma (i.e., DNA that undergoes polyploidization, genome rearrangement, etc.), even in the context of a single nucleus. Here, we extend these arguments by including two well-documented observations: (1) eukaryotic genomes interact frequently with mobile genetic elements (MGEs) like viruses and transposable elements (TEs), creating genetic conflict, and (2) epigenetic mechanisms regulate MGEs. Synthesis of these ideas leads to the hypothesis that genetic conflict with MGEs contributed to the evolution of a dynamic eukaryotic genome in the last eukaryotic common ancestor (LECA), and may have contributed to eukaryogenesis (i.e., may have been a driver in the evolution of FECA, the first eukaryotic common ancestor). Sex (i.e., meiosis) may have evolved within the context of the development of germline-soma distinctions in LECA, as this process resets the germline genome by regulating/eliminating somatic (i.e., polyploid, rearranged) genetic material. Our synthesis of these ideas expands on hypotheses of the origin of eukaryotes by integrating the roles of MGEs and epigenetics.
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Affiliation(s)
- Adena B Collens
- Department of Biological Sciences, Smith College, Northampton, MA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA
- Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA
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18
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Obeng N, Bansept F, Sieber M, Traulsen A, Schulenburg H. Evolution of Microbiota-Host Associations: The Microbe's Perspective. Trends Microbiol 2021; 29:779-787. [PMID: 33674142 DOI: 10.1016/j.tim.2021.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
Microbiota-host associations are ubiquitous in nature. They are often studied using a host-centered view, while microbes are assumed to have coevolved with hosts or colonize hosts as nonadapted entities. Both assumptions are often incorrect. Instead, many host-associated microbes are adapted to a biphasic life cycle in which they alternate between noncoadapted hosts and a free-living phase. Full appreciation of microbiota-host symbiosis thus needs to consider how microbes optimize fitness across this life cycle. Here, we evaluate the key stages of the biphasic life cycle and propose a new conceptual framework for microbiota-host interactions which includes an integrative measure of microbial fitness, related to the parasite fitness parameter R0, and which will help in-depth assessment of the evolution of these widespread associations.
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Affiliation(s)
- Nancy Obeng
- Department of Evolutionary Ecology and Genetics, University of Kiel, Am Botanischen Garten 1- 9, 24118 Kiel, Germany
| | - Florence Bansept
- Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany
| | - Michael Sieber
- Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany
| | - Arne Traulsen
- Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, University of Kiel, Am Botanischen Garten 1- 9, 24118 Kiel, Germany; Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany.
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19
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Füssy Z, Vinopalová M, Treitli SC, Pánek T, Smejkalová P, Čepička I, Doležal P, Hampl V. Retortamonads from vertebrate hosts share features of anaerobic metabolism and pre-adaptations to parasitism with diplomonads. Parasitol Int 2021; 82:102308. [PMID: 33626397 PMCID: PMC7985675 DOI: 10.1016/j.parint.2021.102308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/26/2021] [Accepted: 02/11/2021] [Indexed: 12/17/2022]
Abstract
Although the mitochondria of extant eukaryotes share a single origin, functionally these organelles diversified to a great extent, reflecting lifestyles of the organisms that host them. In anaerobic protists of the group Metamonada, mitochondria are present in reduced forms (also termed hydrogenosomes or mitosomes) and a complete loss of mitochondrion in Monocercomonoides exilis (Metamonada:Preaxostyla) has also been reported. Within metamonads, retortamonads from the gastrointestinal tract of vertebrates form a sister group to parasitic diplomonads (e.g. Giardia and Spironucleus) and have also been hypothesized to completely lack mitochondria. We obtained transcriptomic data from Retortamonas dobelli and R. caviae and searched for enzymes of the core metabolism as well as mitochondrion- and parasitism-related proteins. Our results indicate that retortamonads have a streamlined metabolism lacking pathways for metabolites they are probably capable of obtaining from prey bacteria or their environment, reminiscent of the biochemical arrangement in other metamonads. Retortamonads were surprisingly found do encode homologs of components of Giardia's remarkable ventral disk, as well as homologs of regulatory NEK kinases and secreted lytic enzymes known for involvement in host colonization by Giardia. These can be considered pre-adaptations of these intestinal microorganisms to parasitism. Furthermore, we found traces of the mitochondrial metabolism represented by iron‑sulfur cluster assembly subunits, subunits of mitochondrial translocation and chaperone machinery and, importantly, [FeFe]‑hydrogenases and hydrogenase maturases (HydE, HydF and HydG). Altogether, our results strongly suggest that a remnant mitochondrion is still present.
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Affiliation(s)
- Zoltán Füssy
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic.
| | - Martina Vinopalová
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | | | - Tomáš Pánek
- Charles University, Faculty of Science, Department of Zoology, Prague, Czech Republic
| | - Pavla Smejkalová
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic; Charles University, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | - Ivan Čepička
- Charles University, Faculty of Science, Department of Zoology, Prague, Czech Republic
| | - Pavel Doležal
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic.
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20
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Soluch R, Hülter NF, Romero Picazo D, Özkurt E, Stukenbrock EH, Dagan T. Colonization dynamics of Pantoea agglomerans in the wheat root habitat. Environ Microbiol 2021; 23:2260-2273. [PMID: 33587819 DOI: 10.1111/1462-2920.15430] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/09/2021] [Indexed: 01/27/2023]
Abstract
Plants are colonized by microbial communities that have diverse implications for plant development and health. The establishment of a stable plant-bacteria interaction depends on a continuous coexistence over generations. Transmission via the seed is considered as the main route for vertical inheritance of plant-associated bacteria. Nonetheless, the ecological principles that govern the plant colonization by seed endophytes remain understudied. Here we quantify the contribution of arrival time and colonization history to bacterial colonization of the wheat root. Establishing a common seed endophyte, Pantoea agglomerans, and wheat as a model system enabled us to document bacterial colonization of the plant roots during the early stages of germination. Using our system, we estimate the carrying capacity of the wheat roots as 108 cells g-1 , which is robust among individual plants and over time. Competitions in planta reveal a significant advantage of early incoming colonizers over late-incoming colonizers. Priming for the wheat environment had little effect on the colonizer success. Our experiments thus provide empirical data on the root colonization dynamics of a seed endophyte. The persistence of seed endophyte bacteria with the plant population over generations may contribute to the stable transmission that is one route for the evolution of a stable host-associated lifestyle.
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Affiliation(s)
- Ryszard Soluch
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, 24118, Germany
| | - Nils F Hülter
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, 24118, Germany
| | - Devani Romero Picazo
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, 24118, Germany
| | - Ezgi Özkurt
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, Kiel, 24118, Germany.,Environmental Genomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, 24306, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, Kiel, 24118, Germany.,Environmental Genomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, 24306, Germany
| | - Tal Dagan
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, 24118, Germany
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Hudspith M, Rix L, Achlatis M, Bougoure J, Guagliardo P, Clode PL, Webster NS, Muyzer G, Pernice M, de Goeij JM. Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis. MICROBIOME 2021; 9:44. [PMID: 33583434 PMCID: PMC7883440 DOI: 10.1186/s40168-020-00984-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/16/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea. RESULTS The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome. CONCLUSIONS Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract.
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Affiliation(s)
- Meggie Hudspith
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura Rix
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Michelle Achlatis
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Peta L. Clode
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
- The UWA Oceans Institute, The University of Western Australia, Perth, Australia
- The UWA School of Biological Sciences, The University of Western Australia, Perth, Australia
| | - Nicole S. Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Mathieu Pernice
- Climate Change Cluster (C3), Faculty of Science, University of Technology, Sydney, Australia
| | - Jasper M. de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
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Koskella B, Bergelson J. The study of host-microbiome (co)evolution across levels of selection. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190604. [PMID: 32772660 PMCID: PMC7435161 DOI: 10.1098/rstb.2019.0604] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in the case of host-associated microbiomes-interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host-microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host-microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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Figueiredo ART, Kramer J. Cooperation and Conflict Within the Microbiota and Their Effects On Animal Hosts. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Nalepa CA. Origin of Mutualism Between Termites and Flagellated Gut Protists: Transition From Horizontal to Vertical Transmission. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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