Data from: Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels

Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbor an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found that under light limitation dominant phototrophs, including diatoms and cyanobacteria, displayed a remarkable plasticity in their photosynthetic machinery manifested as higher abundance of messenger RNAs (mRNAs) involved in photosynthesis and chloroplast ribosomal RNA. Under higher light availability, bacterial mRNAs involved in phosphorus metabolism, mainly from Betaproteobacteria and Cyanobacteria, increased, likely compensating for nutrient depletion in thick biofilms with high biomass. Consumers, including diverse ciliates, displayed community shifts indicating preferential grazing on algae instead of bacteria under higher light. For the first time, we show that the functional integrity of stream biofilms under variable light availability is maintained by structure-function adaptations on several trophic levels. Our findings shed new light on complex biofilms, or “microbial jungles”, where in analogy to forests, diverse and multi-trophic level communities lend stability to ecosystem functioning. This multi-trophic level perspective, coupling metatranscriptomics to process measurements, could advance understanding of microbial-driven ecosystems beyond biofilms, including planktonic and soil environments.

光合生物膜（phototrophic biofilms）在淡水与海洋环境中广泛分布，其对于生物地球化学循环、食物网构建以及工业应用均具有关键意义。在溪流生境中，光合生物膜主导着底栖微生物类群，并蕴藏着极为丰富的原核与真核微生物多样性，存在跨域及营养层级的生物相互作用。本研究聚焦于这类生物膜的群落结构与功能如何响应光照条件的变化——光照是光合生物膜赖以生存的核心能量来源。本研究采用宏转录组学（metatranscriptomics）技术开展分析，结果显示：在光照受限条件下，包括硅藻（diatoms）与蓝细菌（cyanobacteria）在内的优势光合生物，其光合系统展现出显著的可塑性，具体表现为参与光合作用的信使RNA（messenger RNA，mRNA）以及叶绿体核糖体RNA的表达丰度显著提升。当光照条件充足时，主要来自β-变形菌门（Betaproteobacteria）与蓝细菌（cyanobacteria）的细菌信使RNA中，参与磷代谢的转录本丰度显著上升，这可能用于弥补高生物量厚生物膜内的营养匮乏状况。包括各类纤毛虫（ciliates）在内的消费者类群，其群落结构发生显著偏移：在光照充足条件下，它们更倾向于摄食藻类而非细菌。本研究首次证实：在光照条件动态变化的环境中，溪流生物膜的功能完整性可通过多营养层级的结构-功能适应性得以维持。本研究结果为解析复杂生物膜（或称"微生物丛林"）提供了新视角：正如森林生态系统一般，多样的多营养层级群落能够为生态系统功能稳定性提供支撑。这种结合宏转录组学技术与过程测量的多营养层级研究视角，不仅可推动对生物膜相关微生物驱动生态系统的认知，还可推广应用于浮游与土壤等其他生态系统。