Aug 2026· Nature Ecology & Evolution· 0 citations· 80 references
Medicine
Abstract
A wide range of microorganisms produce storage biopolymer polyhydroxyalkanoates (sPHAs) as carbon and energy reserves. However, only bacteria and fungi are known to degrade microbial sPHAs, using enzymes called polyhydroxyalkanoate depolymerases (PHADs). Here we show that some animals also have PHADs that can degrade sPHAs. We discovered a PHAD in the gutless oligochaete Olavius algarvensis, a marine worm that gains nutrition by digesting bacterial symbionts, including a dominant symbiont in which sPHAs account for up to 42% of cellular carbon stores. Enzyme assays, combined with mass spectrometry, confirmed that heterologously expressed O. algarvensis PHAD degraded sPHAs into hydroxyalkanoate monomers that can enter conserved metabolic pathways. Imaging of mRNA showed that PHAD was expressed in the oligochaete epidermis, the site of symbiont digestion. We further identified PHADs in more than 66 gut-bearing animal species from nine phyla and 19 protist species from three major supergroups, suggesting that the last common ancestor of metazoans possessed PHADs. Functional assays confirmed that PHADs from phylogenetically distant animal lineages spanning aquatic and terrestrial environments degrade sPHAs. These findings reveal a previously unrecognized pathway by which protists and animals can access microbial carbon reserves, with broad relevance given the widespread occurrence of sPHAs across ecosystems.
Candidatus Hepatincolaceae is a poorly characterized family of obligate Alphaproteobacterial symbionts that are widely detected in ecdysozoans. They were previously assumed to play a nutrient-scavenging role in the gut lumen. In this study, two high-quality metagenome-assembled genomes (MAGs, 1.39 Mb and 1.48 Mb in size) were recovered from the gut of the snapping shrimp Alpheus brevicristatus via metagenomic sequencing. Phylogenetic and whole-genome similarity analyses confirm that these two MAGs represent two novel, undescribed genera within the family Ca. Hepatincolaceae. Metabolic reconstruction reveals that they not only retain the canonical nutrient-scavenging pathways conserved across all Hepatincolaceae members, but also encode previously undocumented functional modules for antioxidant defense, vitamin B1 and B2 biosynthesis, and short-chain fatty acid production. They maintain a high oxygen-affinity cytochrome bd terminal oxidase to thrive in the anoxic gut microenvironment. Consistent with their symbiotic lifestyle, their genomes exhibit typical signatures of reductive evolution, such as reduced genome size, low GC content, and gene loss in amino acid and nucleotide de novo biosynthesis pathways. This study presents the first reported high-quality genomes of marine Ca. Hepatincolaceae symbionts, which are predicted to possess multiple metabolic functions extending beyond nutritional mutualism.
Fangchao Zhu, Yan-Bin Yang, Pei-Pei Liu et al.· Microorganisms· 0 citations
Marine dissolved organic matter (DOM) is a complex pool of substrates, and a central challenge in marine biogeochemistry is to determine which DOM compounds are produced, consumed, or exchanged by microorganisms. Aromatic compounds, including polyphenols, comprise an important chemical class of marine DOM generated both in situ and also supplied via atmospheric deposition, terrestrial runoff, or natural seeps. Here we demonstrate, through pangenomics and metabolic reconstruction, the enrichment of genes for degradation of a wide variety of polyphenols in the cosmopolitan SAR116 bacterioplankton (Puniceispirillales). Gene and pathway conservation, the evolutionary history of key ring-cleaving dioxygenases, and expression patterns from global ocean surveys support the conclusion that these transformations represent core elements of SAR116 ecophysiology. The degradation pathway for protocatechuate, an end member for many polyphenol transformations, occurred in all subclades, and we found evidence of different evolutionary histories for genes in this pathway, including gene loss, analogous substitution, and retention of horizontally transferred genes from the Gammaproteobacteria. Furthermore, variation in these and other pathway-specific gene losses suggest that some SAR116 polyphenol metabolism may occur through a division of labor in concert with other community members and/or require novel or promiscuous enzymes. The enrichment and expression of polyphenol degradation pathways define a previously underappreciated metabolic niche for SAR116 and provides new evidence emphasizing the importance of polyphenol metabolism in the marine carbon cycle.
Jordan T. Coelho, M. Borton, J. Thrash· bioRxiv· 0 citations
Brown algae of the order Dictyotales uniquely stand out among stramenopiles (heterokonts) as prolific producers of bioactive terpenoid molecules associated with chemical defense and antifouling. Although more than 200 sesquiterpenoids and diterpenoids have been reported, largely from the genera of Dictyota and Dictyopteris, their biosynthetic origin has remained unknown for decades. Leveraging de novo genome and transcriptome sequencing in the nonmodel alga Dictyota coriacea, we identified a brown algal-specific lineage of type I terpene synthases (TSs) that harbors novel catalytic motifs distinct from those characterized in plants, microbes, red algae, and metazoans. Across three brown algal species, we characterized 15 terpene synthases, including DcTS-2, which produces the diterpene alcohol dilophol, a proposed biosynthetic intermediate to the antifouling metabolite pachydictyol A. X-ray crystal structures of the monoterpene synthase DcTS-3 further revealed that the brown algal enzymes retain the canonical terpene synthase fold, and together with mutagenesis studies, suggest the catalytic role of the novel motifs defining this newly established evolutionary lineage. Brown algal terpene synthases separate into two subgroups, with mono- and diTSs containing putative chloroplast-targeting sequences while sesquiTSs lack them, suggesting convergent compartmentalization of terpene biosynthesis with land plants. Together, these findings establish the molecular basis of terpenoid biosynthesis in brown algae and highlight the challenges of adapting established biosynthetic logic to nonmodel marine algae.
Hannah K Bone, Jonathan Hsu, Darren C Holland et al.· Journal of the American Chem...· 0 citations
A metagenomic analysis of soil and rhizosphere samples from the Antarctic vascular plants Deschampsia antarctica and Colobanthus quitensis is conducted, as sources of microbial enzymes with potential PET-hydrolytic activity, demonstrating the diversity of PET-hydrolase-like genes within Antarctic rhizosphere and soil microbiomes.
Valentín Berrios-Farías, Sergio Guajardo-Leiva, Jorge Gallardo-Cerda et al.· Frontiers in Microbiology· 0 citations
Growing environmental concerns about conventional plastics have created a demand for alternative resources that are both truly biodegradable and cost-effective. Microbial Polyhydroxyalkanoates (PHAs) are drawing great attention due to their degradability and lower environmental impact on ecosystems. However, higher production cost of bacteria-derived PHAs has become a bottleneck for commercial applications, prompting the search for alternative microbial hosts. Among various microbes, yeasts have become an alternative host for PHAs production due to their stress tolerance, generally regarded as safe (GRAS) status, versatility in substrate utilization, resistance to phage infection, lack of effective biopolymer depolymerizing enzymes and the unique physicochemical environment offered by subcellular compartments for PHAs production. In this perspective, this review provides the current state of PHAs production from wild yeast strains and the various approaches that have been used to improve yield. Furthermore, we discuss the performance, challenges, and limitations of various synthetic biology and metabolic engineering strategies in yeast strains for PHAs production, including overexpressing PHAs biosynthetic genes, knocking out competing pathways, metabolic engineering for precursor supply, and improving renewable feedstock utilization. This review highlights the knowledge gaps in yeast based PHAs production using native and engineered strains, and explains its limitations compared to other microbial sources.
K. Mohanrasu, R. Selvakumar, I. Grainge et al.· International Journal of Bio...· 0 citations
Sulfate-reducing bacteria (SRB) are widespread in marine and terrestrial environments, where they often form syntrophic associations with bacteria, archaea, and eukaryotes. Among the most intimate of these are multipartite symbioses in gutless marine oligochaete worms, which host SRB and sulfur-oxidizing endosymbionts that engage in a syntrophic exchange of sulfur compounds. Despite decades of research on free-living SRB, the metabolic traits that enable SRB to persist in symbiosis, and how these differ across hosts and environments, remain poorly understood. We show that a globally distributed clade of symbiotic SRB, which we named Candidatus Desulfoconcordia, has a conserved core metabolism that diverges from free-living relatives. Using comparative genomics and metaproteomics, we reveal that these endosymbionts retain key traits of SRB such as sulfate reduction, complete oxidation of acetate to CO2, amino acid degradation for nitrogen acquisition, and transport of essential nutrients. However, they exhibit a more oxygen-tolerant metabolism and lack typical nutrient-scavenging mechanisms of free-living SRB. One trait, the glyoxylate bypass, was consistently expressed in situ and may serve both in reactive oxygen species defence and in biomass generation. The expression of oxygen-tolerant pathways, coupled with the loss of nutrient-scavenging functions, indicate specialization to a host-associated, redox-fluctuating environment distinct from that of free-living SRB. The symbiont genomes are also larger than those of free-living relatives, contrasting with genome reduction in many endosymbionts and reinforcing the importance of metabolic versatility. Our findings provide a framework for understanding how metabolic flexibility enables SRB to persist in long-term multipartite symbioses across diverse marine ecosystems.
G. D’Angelo, Manuel Kleiner, A. Mankowski et al.· The ISME Journal· 0 citations