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In response to current threats to salt marshes, there are increasing efforts to restore these vital coastal ecosystems and promote their resilience to global change drivers. Unfortunately, the economic cost associated with assessing the effectiveness of restoration is prohibitive and more information is needed about the trajectory and timing of restoration outcomes to improve restoration practices. Microbial communities provide essential salt marsh functions so assessing the degree to which microbial communities in restored marshes resemble reference marshes can serve as a proxy indicator for the potential return of microbial function. We studied a recently restored marsh located on Cape Cod, MA, USA, by examining shifts in the microbial community and sediment edaphic properties in three habitats of a degraded oligohaline marsh, both before and after restoration of tidal flooding and in comparison with three nearby S. alterniflora reference marshes that never had flow restrictions. We hypothesized that the microbial community would respond rapidly to the restoration and that over time these communities would be indistinguishable from reference marsh communities. We found that soil edaphic characteristics shifted along a trajectory of recovery toward the reference marshes, with increases in salinity and decreases in soil organic matter, percentage of carbon, and percentage of nitrogen. The microbial communities in all three habitats within the restored marsh were different from reference marshes, and both the prokaryotic and fungal communities within P. australis and Typha sp. habitats became more similar to reference marshes (similarities increasing from an average of 5 to 16% for prokaryotes and 3 to 10% for fungi) during the first 2 years after restoration. In that same time period, by contrast, there was no return of the native marsh vegetation. These results suggest that shifts in microbial community structure occur prior to shifts in marsh vegetation and may facilitate the successful revegetation of restored marshes. Understanding the recovery trajectory of marshes during restoration and the role that microbes play in promoting the long-term sustainability of these habitats is essential; these results suggest that microbial communities respond rapidly and in a positive direction to restoration efforts. [ABSTRACT FROM AUTHOR]

Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in microbial communities. Massively parallel DNA sequencing technologies enable extensive surveys of marker gene libraries that sometimes include nearly identical sequences. Computational approaches that rely on pairwise sequence alignments for similarity assessment and de novo clustering with de facto similarity thresholds to partition high-throughput sequencing datasets constrain fine-scale resolution descriptions of microbial communities. Minimum Entropy Decomposition (MED) provides a computationally efficient means to partition marker gene datasets into 'MED nodes', which represent homogeneous operational taxonomic units. By employing Shannon entropy, MED uses only the information-rich nucleotide positions across reads and iteratively partitions large datasets while omitting stochastic variation. When applied to analyses of microbiomes from two deep-sea cryptic sponges Hexadella dedritifera and Hexadella cf. dedritifera, MED resolved a key Gammaproteobacteria cluster into multiple MED nodes that are specific to different sponges, and revealed that these closely related sympatric sponge species maintain distinct microbial communities. MED analysis of a previously published human oral microbiome dataset also revealed that taxa separated by less than 1% sequence variation distributed to distinct niches in the oral cavity. The information theory-guided decomposition process behind the MED algorithm enables sensitive discrimination of closely related organisms in marker gene amplicon datasets without relying on extensive computational heuristics and user supervision. [ABSTRACT FROM AUTHOR]

Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, a single microbial genus that is important for nutrient assimilation as preliminary work suggested host-related patterns within members of this genus. In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping. Our analysis revealed 13 host-specific oligotypes that occurred exclusively in fecal samples of humans (three oligotypes), swine (six oligotypes), cows (one oligotype), deer (one oligotype), or chickens (two oligotypes). We identified an additional 171 oligotypes that exhibited differential abundance patterns among all the host species. Blautia oligotypes in the human population obtained from sewage and fecal samples displayed remarkable continuity. Oligotypes from only 10 Brazilian human fecal samples collected from individuals in a rural village encompassed 97% of all Blautia oligotypes found in a Brazilian sewage sample from a city of three million people. Further, 75% of the oligotypes in Brazilian human fecal samples matched those in US sewage samples, implying that a universal set of Blautia strains may be shared among culturally and geographically distinct human populations. Such strains can serve as universal markers to assess human fecal contamination in environmental samples. Our results indicate that host-specificity and host-preference patterns of organisms within this genus are driven by host physiology more than dietary habits. [ABSTRACT FROM AUTHOR]