A rapid fingerprinting approach to distinguish between closely related strains of Shewanella

Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution

Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.

Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems

Ancient DNA (aDNA) analysis of lake sediments is a promising tool for detecting shifts in past microbial assemblages in response to changing environmental conditions. We examined sediment core samples from subtropical, freshwater Laguna Blanca (Uruguay), which has been severely affected by cultural eutrophication since 1960 and where cyanobacterial blooms, particularly those of the saxitoxin-producer Cylindrospermopsis raciborskii, have been reported since the 1990s. Samples corresponding to ~1846, 1852, 2000 and 2007 AD were selected to perform denaturing gradient gel electrophoresis (DGGE) analysis of the 16S-23S rRNA intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic assemblage composition. Each stratum showed different ITS patterns, but the composition of 21st century samples was clearly different than those of mid-19th century. This compositional change was correlated with shifts in sediment organic matter and chlorophyll a content, which were significantly higher in recent samples. The presence of saxitoxin-producing cyanobacteria was addressed by quantitative real-time PCR of the sxtU gene involved in toxin biosynthesis. This gene was present only in recent samples, for which clone libraries and ITS sequencing indicated the presence of Cyanobacteria. Phylogenetic analyses identified C. raciborskii only in the 2000 sample, shortly after several years when blooms were recorded in the lake. These data suggest the utility of aDNA for the reconstruction of microbial assemblage shifts in subtropical lakes, at least on centennial scales. The application of aDNA analysis to genes involved in cyanotoxin synthesis extends the applicability of molecular techniques in palaeolimnological studies to include key microbial community characteristics of great scientific and social interest.