Publications

4477

Abstract Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.

Abstract Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood–Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.

Abstract‘Candidatus Phytoplasma meliae’ (subgroups 16SrXIII-G and XIII-C) has been reported in association to chinaberry yellowing disease in Argentina, Bolivia and Paraguay. In Argentina, this disease constitutes a major phytosanitary problem for chinaberry forestry production. To date, no genome information of this phytoplasma and others from 16SrXIII-group has been published, hindered its characterization at genomic level. Here we analyze the draft genome of ‘Candidatus Phytoplasma meliae’ strain ChTYXIII obtained from a chinaberry-infected plant using a metagenomics approach. The draft assembly consists of twenty-one contigs with a total length of 751.949 bp. The annotation contains 669 CDSs, 34tRNA and one set of rRNA operons. Metabolic pathways analysis indicated that the ChTYXIII contains the complete core genes for glycolysis and functional sec system for translocation of proteins. The phylogenetic relationships inferred 132 single copy genes (orthologues core) analysis revealed that ‘Ca. P. meliae’ constitutes a clade closely related to the ‘Ca. australiense’ and ‘Ca. P. solani’. Thirty-one putative effectors were identified, among which a homologue to SAP11 was found and others that have only been described in this pathogen. This work provides relevant genomic information for ‘Ca. P. meliae’ and constitutes the first genome described for the group 16SrXIII (MPV).

AbstractThe olive fruit fly, Bactrocera oleae, the most serious pest of olives, requires the endosymbiotic bacteria Candidatus Erwinia dacicola in order to complete its development in unripe green olives. Hence a better understanding of the symbiosis of Ca. E. dacicola and its insect host may lead to new strategies for reduction of B. oleae and thus minimize its economic impact on olive production. Studies of this symbiosis are hampered as the bacterium cannot be grown in vitro and the established B. oleae laboratory populations, raised on artificial diets, are devoid of this bacterium. Here, we sought to develop a method to transfer the bacteria from wild samples to laboratory populations. We tested several strategies. Cohabitation of flies from the field with the laboratory line did not result in a stable transfer of bacteria. We provided the bacteria directly to the egg and also in the food of the larvae but neither approach was successful. However, a robust method for transfer of Ca. E. dacicola from wild larvae or adults to uninfected flies by transplantation to females was established. Single female lines were set up and the bacteria were successfully transmitted for at least three generations. These results open up the possibilities to study the interaction between the symbiont and the host under controlled conditions, in view of both understanding the molecular underpinnings of an exciting, unique in nature symbiotic relationship, as well as developing novel, innovative control approaches.

Abstract Phytoplasmas are wall-less parasitic bacteria living exclusively in plant phloem as consequence of transmission by sap-sucking insect vectors (Lee et al., 2000); they have been associated with several hundred plant diseases. 'Candidatus Phytoplasma phoenicium' (CaPphoe), subgroup 16SrIX-B, is the aetiological agent of almond witches'-broom (AlmWB), a severe disease affecting almond, peach and nectarine trees in Lebanon and Iran. The first epidemics of AlmWB occurred in almond trees in Lebanon in the early 1990s and in Iran in 1995. In Lebanon, the disease rapidly spread from coastal to high mountainous areas, killing almost 150,000 trees over a period of 15 years. CaPphoe was first added to the EPPO Alert List in 2001 and removed from the list in 2006. The more recent rapid spread of CaPphoe in peach and nectarine orchards and in other plant hosts, along with the identification of efficient insect vectors, increased the alarm about the risk it poses for stone fruit production in the Middle East and in all the countries of the Mediterranean basin. Thus it was re-inserted in the EPPO Alert List in 2015.

The cyanobacterial genus Nostoc is an important contributor to carbon and nitrogen bioavailability in terrestrial ecosystems and a frequent partner in symbiotic relationships with non-diazotrophic organisms. However, since this currently is a polyphyletic genus, the diversity of Nostoc -like cyanobacteria is considerably underestimated at this moment. While reviewing the phylogenetic placement of previously isolated Nostoc -like cyanobacteria originating from Brazilian Amazon, Caatinga and Atlantic forest samples, we detected 17 strains isolated from soil, freshwater, rock and tree surfaces presenting patterns that diverged significantly from related strains when ecological, morphological, molecular and genomic traits were also considered. These observations led to the identification of the evaluated strains as representative of three novel nostocacean genera and species: Amazonocrinis nigriterrae gen. nov., sp. nov.; Atlanticothrix silvestris gen. nov., sp. nov.; and Dendronalium phyllosphericum gen. nov., sp. nov., which are herein described according to the rules of the International Code of Nomenclature for algae, fungi and plants. This finding highlights the great importance of tropical and equatorial South American ecosystems for harbouring an unknown microbial diversity in the face of the anthropogenic threats with which they increasingly struggle.

Abstract 'Ca. Phytoplasma pini' is a member of phytoplasma 16S rRNA gene RFLP group XXI, subgroup XXI-A. It has been identified in a number of European countries, including Germany, Poland, Lithuania, Spain, Czech Republic and Croatia. Outside of Europe it has been identified in China and Mozambique. A related strain has also been identified in Maryland, USA. In the USA, favourable climatic conditions and wide availability of potential host plants of the phytoplasma, suggest that the potential for spread of 'Ca. Phytoplasma pini' could be significant. Host plants include Pinus sylvestris, P. halepensis, P. mugo, P. banksiana, P. nigra, P. tabuliformis, Abies procera and Tsuga canadensis. Symptoms include the formation of ball-like growths containing dwarfed needles, yellowed or reddish needles and the loss of needles. It is transmitted by insect vectors that are currently unknown.

AbstractBackgroundIn gut microbiome studies, the cultured gut microbial resource plays essential roles, such as helping to unravel gut microbial functions and host-microbe interactions. Although several major studies have been performed to elucidate the cultured human gut microbiota, up to 70% of the Unified Human Gastrointestinal Genome species have not been cultured to date. Large-scale gut microbial isolation and identification as well as availability to the public are imperative for gut microbial studies and further characterizing human gut microbial functions.ResultsIn this study, we constructed a human Gut Microbial Biobank (hGMB; homepage:hgmb.nmdc.cn) through the cultivation of 10,558 isolates from 31 sample mixtures of 239 fresh fecal samples from healthy Chinese volunteers, and deposited 1170 strains representing 400 different species in culture collections of the International Depository Authority for long-term preservation and public access worldwide. Following the rules of the International Code of Nomenclature of Prokaryotes, 102 new species were characterized and denominated, while 28 new genera and 3 new families were proposed. hGMB represented over 80% of the common and dominant human gut microbial genera and species characterized from global human gut 16S rRNA gene amplicon data (n= 11,647) and cultured 24 “most-wanted” and “medium priority” taxa proposed by the Human Microbiome Project. We in total sequenced 115 genomes representing 102 novel taxa and 13 previously known species. Further in silico analysis revealed that the newly sequenced hGMB genomes represented 22 previously uncultured species in the Unified Human Gastrointestinal Genome (UHGG) and contributed 24 representatives of potentially “dark taxa” that had not been discovered by UHGG. The nonredundant gene catalogs generated from the hGMB genomes covered over 50% of the functionally known genes (KEGG orthologs) in the largest global human gut gene catalogs and approximately 10% of the “most wanted” functionally unknown proteins in the FUnkFams database.ConclusionsA publicly accessible human Gut Microbial Biobank (hGMB) was established that contained 1170 strains and represents 400 human gut microbial species. hGMB expands the gut microbial resources and genomic repository by adding 102 novel species, 28 new genera, 3 new families, and 115 new genomes of human gut microbes.