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.

光养生物膜（phototrophic biofilms）广泛分布于淡水与海洋环境中，其在生物地球化学循环、食物网构建以及工业应用中均发挥着关键作用。在溪流生境中，光养生物膜主导着底栖微生物群落，蕴含着极为丰富的原核与真核微生物多样性，并存在跨域及跨营养级的生物相互作用。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强度的变化——光照正是光养生物膜的核心能量来源。通过宏转录组学（metatranscriptomics）分析，我们发现：在光照受限条件下，包括硅藻（diatoms）与蓝细菌（cyanobacteria）在内的优势光养微生物，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。在光照充足条件下，主要来自β-变形菌门（Betaproteobacteria）与蓝细菌的、参与磷代谢的细菌mRNA表达量显著上调，这很可能是为了补偿高生物量厚生物膜中的营养元素匮乏。包括多种纤毛虫（ciliates）在内的消费者类群则出现了群落结构转变，表明在光照充足时它们更倾向于捕食藻类而非细菌。本研究首次证实，溪流生物膜在光照波动下的功能完整性，是通过多个营养级上的结构-功能适应性调控得以维持的。我们的研究结果为复杂生物膜——即被称为"microbial jungles"的群落——带来了新的认知视角：正如森林生态系统一般，多样的跨营养级群落能够为生态系统功能提供稳定性。这种结合宏转录组学与过程测定的跨营养级研究视角，不仅能够深化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。