Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001, Lisbon, Portugal.
Laboratory of Aquatic Systems Ecology, Université Libre de Bruxelles, Brussels, Belgium.
Microbiome. 2021 Feb 14;9(1):43. doi: 10.1186/s40168-020-00970-2.
Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater.
We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates.
Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.
甲壳素是海洋中最丰富的多糖之一，但对于海洋小生境中甲壳素降解群落结构和多样性的变化知之甚少。在这里，我们整合了依赖和独立于培养的方法，以揭示海洋海绵、八放珊瑚、沉积物和海水中微生物组中甲壳素加工的潜力。
我们发现，在 Aquimarina、Enterovibrio、Microbulbifer、Pseudoalteromonas、Shewanella 和 Vibrio 属中可培养的宿主相关细菌能够在体外降解胶体甲壳素。与酶活性生物测定一致，对培养共生体的全基因组检查表明，特别是 Vibrio 和 Aquimarina 物种，具有几种内切和外切甲壳素酶编码基因，使其能够将大的甲壳素聚合物切割成低聚物和二聚体。相反，α变形菌物种更倾向于利用甲壳素单体 N-乙酰氨基葡萄糖。系统发育评估揭示了 Aquimarina 和 Vibrio 菌株中多个全长内切甲壳素酶基因的高度基因组内多样化，表明其具有多功能的甲壳素分解代谢能力。然后，我们分析了 30 个 Illumina 测序微生物宏基因组中与甲壳素代谢相关基因的丰度分布，发现 Spongia officinalis 的内共生体 consortium富含多糖去乙酰化酶，表明海洋海绵微生物组将甲壳素转化为其去乙酰化和具有生物技术多功能形式壳聚糖的能力。相反，健康八放珊瑚中内切甲壳素酶和甲壳素结合蛋白编码基因的丰度与周围环境中的丰度持平，但在坏死八放珊瑚组织中发现其耗尽。使用非培养的、基于分类学的内切甲壳素酶编码基因的分配，我们揭示了以前未被怀疑的、宿主相关和自由生活生物区系中甲壳素分解群落的丰富度和不同结构，表明未培养的γ变形菌和绿弯菌门共生体在附着海洋无脊椎动物中的甲壳素加工中可能发挥作用。
我们的研究结果表明，不同的甲壳素降解途径、利用和周转决定了海洋小生境中甲壳素的加工，并支持种间交叉喂养可以促进海洋无脊椎动物微生物组中甲壳素利用者共存的假说。我们进一步确定了可能作为珊瑚微生物组完整性/功能障碍的指标的甲壳素代谢功能，并揭示了 Aquimarina 属中可能在蓝色生物技术领域有应用的新型甲壳素水解酶。视频摘要。
