1
|
Coevolution of Metabolic Pathways in Blattodea and Their Blattabacterium Endosymbionts, and Comparisons with Other Insect-Bacteria Symbioses. Microbiol Spectr 2022; 10:e0277922. [PMID: 36094208 PMCID: PMC9603385 DOI: 10.1128/spectrum.02779-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Many insects harbor bacterial endosymbionts that supply essential nutrients and enable their hosts to thrive on a nutritionally unbalanced diet. Comparisons of the genomes of endosymbionts and their insect hosts have revealed multiple cases of mutually-dependent metabolic pathways that require enzymes encoded in 2 genomes. Complementation of metabolic reactions at the pathway level has been described for hosts feeding on unbalanced diets, such as plant sap. However, the level of collaboration between symbionts and hosts that feed on more variable diets is largely unknown. In this study, we investigated amino acid and vitamin/cofactor biosynthetic pathways in Blattodea, which comprises cockroaches and termites, and their obligate endosymbiont Blattabacterium cuenoti (hereafter Blattabacterium). In contrast to other obligate symbiotic systems, we found no clear evidence of "collaborative pathways" for amino acid biosynthesis in the genomes of these taxa, with the exception of collaborative arginine biosynthesis in 2 taxa, Cryptocercus punctulatus and Mastotermes darwiniensis. Nevertheless, we found that several gaps specific to Blattabacterium in the folate biosynthetic pathway are likely to be complemented by their host. Comparisons with other insects revealed that, with the exception of the arginine biosynthetic pathway, collaborative pathways for essential amino acids are only observed in phloem-sap feeders. These results suggest that the host diet is an important driving factor of metabolic pathway evolution in obligate symbiotic systems. IMPORTANCE The long-term coevolution between insects and their obligate endosymbionts is accompanied by increasing levels of genome integration, sometimes to the point that metabolic pathways require enzymes encoded in two genomes, which we refer to as "collaborative pathways". To date, collaborative pathways have only been reported from sap-feeding insects. Here, we examined metabolic interactions between cockroaches, a group of detritivorous insects, and their obligate endosymbiont, Blattabacterium, and only found evidence of collaborative pathways for arginine biosynthesis. The rarity of collaborative pathways in cockroaches and Blattabacterium contrasts with their prevalence in insect hosts feeding on phloem-sap. Our results suggest that host diet is a factor affecting metabolic integration in obligate symbiotic systems.
Collapse
|
2
|
Vasquez YM, Bennett GM. A complex interplay of evolutionary forces continues to shape ancient co-occurring symbiont genomes. iScience 2022; 25:104786. [PMID: 35982793 PMCID: PMC9379567 DOI: 10.1016/j.isci.2022.104786] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/03/2022] [Accepted: 07/13/2022] [Indexed: 01/03/2023] Open
Abstract
Many insects depend on ancient associations with intracellular bacteria for essential nutrition. The genomes of these bacteria are often highly reduced. Although drift is a major driver of symbiont evolution, other evolutionary forces continue to influence them. To understand how ongoing molecular evolution and gene loss shape symbiont genomes, we sequenced two of the most ancient symbionts known, Sulcia and Nasuia, from 20 Hawaiian Nesophrosyne leafhoppers. We leveraged the parallel divergence of Nesophrosyne lineages throughout Hawaii as a natural experimental framework. Sulcia and Nasuia experience ongoing-but divergent-gene loss, often in a convergent fashion. Although some genes are under relaxed selection, purifying and positive selection are also important drivers of genome evolution, particularly in maintaining certain nutritional and cellular functions. Our results further demonstrate that symbionts experience dramatically different evolutionary environments, as evidenced by the finding that Sulcia and Nasuia have one of the slowest and fastest rates of molecular evolution known.
Collapse
Affiliation(s)
- Yumary M. Vasquez
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| | - Gordon M. Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| |
Collapse
|
3
|
Cao Y, Dietrich CH. Phylogenomics of flavobacterial insect nutritional endosymbionts with implications for Auchenorrhyncha phylogeny. Cladistics 2021; 38:38-58. [DOI: 10.1111/cla.12474] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yanghui Cao
- Illinois Natural History Survey Prairie Research Institute University of Illinois Champaign IL61820USA
| | - Christopher H. Dietrich
- Illinois Natural History Survey Prairie Research Institute University of Illinois Champaign IL61820USA
| |
Collapse
|
4
|
Abstract
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the set of capabilities that enables a population's persistence and defines its impact on the environment. The set of possible niches forms the niche space, a conceptual space delineating ways in which persistence in a system is possible. Here we use manifold learning to map the space of metabolic networks representing thousands of bacterial genera. The results suggest a metabolic niche space comprising a collection of discrete clusters and branching manifolds, which constitute strategies spanning life in different habitats and hosts. We further demonstrate that communities from similar ecosystem types map to characteristic regions of this functional coordinate system, permitting coarse-graining of microbiomes in terms of ecological niches that may be filled.
Collapse
Affiliation(s)
- Ashkaan K Fahimipour
- University of California Davis, Department of Computer Science, 1 Shields Ave, Davis, CA, 95616, USA.
- National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, 110 McAllister Way, Santa Cruz, CA, 95060, USA.
| | - Thilo Gross
- University of California Davis, Department of Computer Science, 1 Shields Ave, Davis, CA, 95616, USA
- Alfred-Wegener-Institut Helmholtz-Centre for Marine and Polar Research, AM Handelshafen 12, Bremerhaven, 27570, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Ammerländer Heerstrasse 231, 26129, Oldenburg, Germany
- University of Oldenburg, Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky Str. 9 - 11, 26129, Oldenburg, Germany
| |
Collapse
|
5
|
Abstract
Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.
Collapse
|
6
|
Gil R, Latorre A. Unity Makes Strength: A Review on Mutualistic Symbiosis in Representative Insect Clades. Life (Basel) 2019; 9:E21. [PMID: 30823538 PMCID: PMC6463088 DOI: 10.3390/life9010021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/11/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Settled on the foundations laid by zoologists and embryologists more than a century ago, the study of symbiosis between prokaryotes and eukaryotes is an expanding field. In this review, we present several models of insect⁻bacteria symbioses that allow for the detangling of most known features of this distinctive way of living, using a combination of very diverse screening approaches, including molecular, microscopic, and genomic techniques. With the increasing the amount of endosymbiotic bacteria genomes available, it has been possible to develop evolutionary models explaining the changes undergone by these bacteria in their adaptation to the intracellular host environment. The establishment of a given symbiotic system can be a root cause of substantial changes in the partners' way of life. Furthermore, symbiont replacement and/or the establishment of bacterial consortia are two ways in which the host can exploit its interaction with environmental bacteria for endosymbiotic reinvigoration. The detailed study of diverse and complex symbiotic systems has revealed a great variety of possible final genomic products, frequently below the limit considered compatible with cellular life, and sometimes with unanticipated genomic and population characteristics, raising new questions that need to be addressed in the near future through a wider exploration of new models and empirical observations.
Collapse
Affiliation(s)
- Rosario Gil
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC. Calle Catedrático Agustín Escardino, 9, 46980 Paterna (Valencia), Spain.
- Departament de Genètica, Universitat de València. Calle Dr. Moliner, 50, 46100 Burjassot (València), Spain.
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO). Avenida de Cataluña 21, 46020 València, Spain.
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC. Calle Catedrático Agustín Escardino, 9, 46980 Paterna (Valencia), Spain.
- Departament de Genètica, Universitat de València. Calle Dr. Moliner, 50, 46100 Burjassot (València), Spain.
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO). Avenida de Cataluña 21, 46020 València, Spain.
| |
Collapse
|
7
|
Bennett GM, Mao M. Comparative genomics of a quadripartite symbiosis in a planthopper host reveals the origins and rearranged nutritional responsibilities of anciently diverged bacterial lineages. Environ Microbiol 2018; 20:4461-4472. [PMID: 30047196 DOI: 10.1111/1462-2920.14367] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/15/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
Insects in the Auchenorrhyncha (Hemiptera: Suborder) established nutritional symbioses with bacteria approximately 300 million years ago (MYA). The suborder split early during its diversification (~ 250 MYA) into the Fulgoroidea (planthoppers) and Cicadomorpha (leafhoppers and cicadas). The two lineages share some symbionts, including Sulcia and possibly a Betaproteobacteria that collaboratively provide their hosts with 10 essential amino acids (EAA). Some hosts harbour three bacteria, as is common among planthoppers. However, genomic studies are currently restricted to the dual-bacterial symbioses found in Cicadomorpha, leaving the origins and functions of these more complex symbioses unclear. To address these questions, we sequenced the genomes and performed phylogenomic analyses of 'Candidatus Sulcia muelleri' (Bacteroidetes), 'Ca. Vidania fulgoroideae' (Betaproteobacteria) and 'Ca. Purcelliella pentastirinorum' (Gammaproteobacteria) from a planthopper (Cixiidae: Oliarus). In contrast to the Cicadomorpha, nutritional synthesis responsibilities are rearranged between the cixiid symbionts. Although Sulcia has a highly conserved genome across the Auchenorrhyncha, in the cixiids it is greatly reduced and provides only three EAAs. Vidania contributes the remaining seven EAAs. Phylogenomic results suggest that it represents an ancient symbiont lineage paired with Sulcia throughout the Auchenorrhyncha. Finally, Purcelliella was recently acquired from plant-insect associated bacteria (Pantoea-Erwinia) to provide B vitamins and metabolic support to its degenerate partners.
Collapse
Affiliation(s)
- Gordon M Bennett
- Life and Environmental Sciences Unit, University of California, Merced, CA, 95343, USA.,Department of Plant and Environmental Protections Sciences, University of Hawaii at Mānoa, Honolulu, HI, 96822, USA
| | - Meng Mao
- Life and Environmental Sciences Unit, University of California, Merced, CA, 95343, USA.,Department of Plant and Environmental Protections Sciences, University of Hawaii at Mānoa, Honolulu, HI, 96822, USA
| |
Collapse
|
8
|
Mao M, Yang X, Poff K, Bennett G. Comparative Genomics of the Dual-Obligate Symbionts from the Treehopper, Entylia carinata (Hemiptera: Membracidae), Provide Insight into the Origins and Evolution of an Ancient Symbiosis. Genome Biol Evol 2017; 9:1803-1815. [PMID: 28854637 PMCID: PMC5533117 DOI: 10.1093/gbe/evx134] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2017] [Indexed: 12/20/2022] Open
Abstract
Insect species in the Auchenorrhyncha suborder (Hemiptera) maintain ancient obligate symbioses with bacteria that provide essential amino acids (EAAs) deficient in their plant-sap diets. Molecular studies have revealed that two complementary symbiont lineages, "Candidatus Sulcia muelleri" and a betaproteobacterium ("Ca. Zinderia insecticola" in spittlebugs [Cercopoidea] and "Ca. Nasuia deltocephalinicola" in leafhoppers [Cicadellidae]) may have persisted in the suborder since its origin ∼300 Ma. However, investigation of how this pair has co-evolved on a genomic level is limited to only a few host lineages. We sequenced the complete genomes of Sulcia and a betaproteobacterium from the treehopper, Entylia carinata (Membracidae: ENCA), as the first representative from this species-rich group. It also offers the opportunity to compare symbiont evolution across a major insect group, the Membracoidea (leafhoppers + treehoppers). Genomic analyses show that the betaproteobacteria in ENCA is a member of the Nasuia lineage. Both symbionts have larger genomes (Sulcia = 218 kb and Nasuia = 144 kb) than related lineages in Deltocephalinae leafhoppers, retaining genes involved in basic cellular functions and information processing. Nasuia-ENCA further exhibits few unique gene losses, suggesting that its parent lineage in the common ancestor to the Membracoidea was already highly reduced. Sulcia-ENCA has lost the abilities to synthesize menaquinone cofactor and to complete the synthesis of the branched-chain EAAs. Both capabilities are conserved in other Sulcia lineages sequenced from across the Auchenorrhyncha. Finally, metagenomic sequencing recovered the partial genome of an Arsenophonus symbiont, although it infects only 20% of individuals indicating a facultative role.
Collapse
Affiliation(s)
- Meng Mao
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| | - Xiushuai Yang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| | - Kirsten Poff
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| | - Gordon Bennett
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Mānoa
| |
Collapse
|
9
|
Brentassi ME, Franco E, Balatti P, Medina R, Bernabei F, Marino de Remes Lenicov AM. Bacteriomes of the corn leafhopper, Dalbulus maidis (DeLong & Wolcott, 1923) (Insecta, Hemiptera, Cicadellidae: Deltocephalinae) harbor Sulcia symbiont: molecular characterization, ultrastructure, and transovarial transmission. PROTOPLASMA 2017; 254:1421-1429. [PMID: 27730310 DOI: 10.1007/s00709-016-1033-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
In this study, we surveyed the bacteriome-associated microbiota of the corn leafhopper Dalbulus maidis by means of histological, ultrastructural, and molecular analyses. Amplification and sequencing of 16S rDNA genes revealed that the endosymbiont "Candidatus Sulcia muelleri" (Phylum Bacteroidetes) resides in bacteriomes of D. maidis. Phylogenetic analysis showed that the sequence was closely allied to others found in representatives of the subfamily Deltocephalinae. We failed to amplify other sequences as "Candidatus Nasuia deltocephalinicola," a co-primary symbiont frequently associated to deltocephaline leafhoppers. In addition, a metagenetic analysis carried out in order to investigate the presence of other bacteriome-associated bacteria of D. maidis showed that the sequence of Sulcia accounted for 98.56 % of all the sequences. Histological and ultrastructural observations showed that microorganisms harbored in bacteriomes (central syncytium and cytoplasm of uninucleate bacteriocytes) look like others Sulcia described in hemipteran species and they were transovarially transmitted from mother to offspring which is typical of obligate endosymbionts. The only presence of Sulcia in the bacteriomes of D. maidis was discussed.
Collapse
Affiliation(s)
- María Eugenia Brentassi
- División Entomología. Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (UNLP), 1900, La Plata, Argentina.
- Comisión de Investigaciones Científicas, Pcia de Bs. As. (CIC) and Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), La Plata, Argentina.
| | - Ernesto Franco
- Centro de Investigaciones de Fitopatología (CIDEFI). Facultad de Ciencias Agrarias y Forestales, UNLP-CIC, La Plata, Argentina
| | - Pedro Balatti
- Centro de Investigaciones de Fitopatología (CIDEFI). Facultad de Ciencias Agrarias y Forestales, UNLP-CIC, La Plata, Argentina
| | - Rocío Medina
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI). Facultad de Ciencias Exactas, UNLP-CONICET, La Plata, Argentina
| | - Franco Bernabei
- Centro de Investigaciones de Fitopatología (CIDEFI). Facultad de Ciencias Agrarias y Forestales, UNLP-CIC, La Plata, Argentina
| | - Ana M Marino de Remes Lenicov
- División Entomología. Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (UNLP), 1900, La Plata, Argentina
- Comisión de Investigaciones Científicas, Pcia de Bs. As. (CIC) and Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), La Plata, Argentina
| |
Collapse
|
10
|
Complete Genome Sequences of the Obligate Symbionts "Candidatus Sulcia muelleri" and "Ca. Nasuia deltocephalinicola" from the Pestiferous Leafhopper Macrosteles quadripunctulatus (Hemiptera: Cicadellidae). GENOME ANNOUNCEMENTS 2016; 4:4/1/e01604-15. [PMID: 26798106 PMCID: PMC4722273 DOI: 10.1128/genomea.01604-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two bacterial symbionts of the European pest leafhopper, Macrosteles quadripunctulatus (Hemiptera: Cicadellidae), were fully sequenced. “Candidatus Sulcia muelleri” and “Ca. Nasuia deltocephalinicola” represent two of the smallest known bacterial genomes at 190 kb and 112 kb, respectively. Genome sequences are nearly identical to strains reported from the closely related host species, M. quadrilineatus.
Collapse
|
11
|
Bennett GM, McCutcheon JP, McDonald BR, Moran NA. Lineage-Specific Patterns of Genome Deterioration in Obligate Symbionts of Sharpshooter Leafhoppers. Genome Biol Evol 2015; 8:296-301. [PMID: 26260652 PMCID: PMC4758232 DOI: 10.1093/gbe/evv159] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plant sap-feeding insects (Hemiptera) rely on obligate bacterial symbionts that provision nutrients. Some of these symbionts are ancient and have evolved tiny genomes, whereas others are younger and retain larger, dynamic genomes. Baumannia cicadellinicola, an obligate symbiont of sharpshooter leafhoppers, is derived from a relatively recent symbiont replacement. To better understand evolutionary decay of genomes, we compared Baumannia from three host species. A newly sequenced genome for Baumannia from the green sharpshooter (B-GSS) was compared with genomes of Baumannia from the blue-green sharpshooter (B-BGSS, 759 kilobases [kb]) and from the glassy-winged sharpshooter (B-GWSS, 680 kb). B-GSS has the smallest Baumannia genome sequenced to date (633 kb), with only three unique genes, all involved in membrane function. It has lost nearly all pathways involved in vitamin and cofactor synthesis, as well as amino acid biosynthetic pathways that are redundant with pathways of the host or the symbiotic partner, Sulcia muelleri. The entire biosynthetic pathway for methionine is eliminated, suggesting that methionine has become a dietary requirement for hosts. B-GSS and B-BGSS share 33 genes involved in bacterial functions (e.g., cell division, membrane synthesis, metabolite transport, etc.) that are lost from the more distantly related B-GWSS and most other tiny genome symbionts. Finally, pairwise divergence estimates indicate that B-GSS has experienced a lineage-specific increase in substitution rates. This increase correlates with accelerated protein-level changes and widespread gene loss. Thus, the mode and tempo of genome reduction vary widely among symbiont lineages and result in wide variation in metabolic capabilities across hosts.
Collapse
Affiliation(s)
- Gordon M Bennett
- Department of Integrative Biology, University of Texas, Austin Department of Plant and Environmental Protection Sciences, University of Hawaii, Manoa
| | | | | | - Nancy A Moran
- Department of Integrative Biology, University of Texas, Austin Institute for Cellular and Molecular Biology, University of Texas, Austin
| |
Collapse
|
12
|
Abstract
Agrobacterium tumefaciens is a phytopathogenic bacterium that causes crown gall disease. The strain Ach5 was isolated from yarrow (Achillea ptarmica L.) and is the wild-type progenitor of other derived strains widely used for plant transformation. Here, we report the complete genome sequence of this bacterium.
Collapse
|