Gilbert Naomi E, Kimbrel Jeffrey A, Samo Ty J, Siccardi Anthony J, Stuart Rhona K, Mayali Xavier
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA.
Department of Biology, Georgia Southern University, Statesboro, Georgia, USA.
mSystems. 2025 Jun 17;10(6):e0037525. doi: 10.1128/msystems.00375-25. Epub 2025 May 14.
Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, grown in outdoor ponds. 16S rRNA gene data indicated that a single sp. strain (family ) contributed up to 93% of the bacterial community during demise. sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. and laboratory data with a different strain suggested that was a primary degrader of biopolymers during algal demise, and co-occurring exploited degradation molecules for carbon. An analysis of 30 metagenome assembled genomes suggested that algal pond commonly harbored pathways to use diverse carbon and energy sources including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom . Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.
以藻类为主导的生态系统从根本上受到其微生物群落的影响。对于在高藻类密度生态系统（如用于生物燃料生产的室外藻池）中专门消耗藻类衍生溶解有机物的细菌的身份和功能，我们尚缺乏相关信息。在此，我们描述了一种单一细菌菌株的宏基因组和宏蛋白质组特征，该菌株在室外池塘中生长的硅藻种群大规模崩溃期间大量繁殖。16S rRNA基因数据表明，在硅藻死亡期间，一种单一的菌株（属 科）在细菌群落中所占比例高达93%。该菌株表达了与微生物拮抗作用和生物聚合物分解相关的蛋白质，这可能是其在硅藻死亡期间相对于其他微生物类群占据优势的原因。对伴随的下游微生物群（主要是 科）的分析提供了证据，表明交叉喂养可能是硅藻死亡期间支持微生物多样性的一条途径。来自不同菌株的现场和实验室数据表明，该菌株是藻类死亡期间生物聚合物的主要降解者，同时存在的 菌利用降解产物获取碳源。对30个宏基因组组装基因组的分析表明，藻池 通常拥有利用包括一氧化碳在内的多种碳源和能源的途径，这可能是该分类群在池塘中普遍存在的原因。这些观察结果进一步明确了功能不同的异养细菌在藻类微生物群落中的作用，展示了一种专门处理衰老或死亡藻类生物量的单一优势细菌如何塑造室外藻类生物燃料池塘的微生物群落。重要性水生生物地球化学循环由栖息在藻类微生物群落中的各种微生物的活动所决定。室外生物燃料池塘提供了一个类似于水华的环境，在那里快速生长的藻类单一培养物达到高细胞密度。目前缺乏关于这种环境下微生物生态学的信息，因此我们采用宏基因组学和宏蛋白质组学来了解接种了硅藻的四个重复室外池塘中存在的细菌的代谢作用。出乎意料的是，经过29天的培养，所有四个池塘同时崩溃，伴随着一种属于 细菌属的单一分类群的“大量繁殖”。我们评估了这种优势分类群在崩溃后如何影响池塘的化学和微生物命运，假设它主要负责处理衰老/死亡的藻类生物量并为周围的微生物群提供碳源。总体而言，这些发现深入了解了专门处理藻类有机物的微生物的作用，并增强了我们对生物燃料池塘微生物生态学的理解。
