Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data.

Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13−26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.

Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic “continents,” indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation. Microorganisms from the bacterial and archaeal domains of the tree of life comprise the greatest breadth of biodiversity on earth. Yet the essential evolutionary process of speciation (through which biodiversity is generated) is poorly understood in microbes. At issue is the fundamental question of whether gene flow among individuals of clonally reproducing microorganisms is rapid enough to provide coherence within—and prevent speciation between—coexisting lineages. We use complete sequencing of microbial genomes to observe speciation in action. We focus on Archaea called Sulfolobus islandicus gathered from a geothermal hot spring from the Mutnovsky Volcano in Kamchatka, Russia, whose physical isolation allows us to pinpoint evolutionary processes to one location. Contrary to the theoretical predictions for microbes, we provide evidence that two novel lineages are in the process of becoming ecologically distinct and evolutionarily independent despite the fact that they recombine. The divergence we observe is not happening uniformly across the genome because certain genomic regions are more prone to become differentiated between species than others. This genomic view of the process of speciation occurring within a single natural microbial population contributes to our understanding of the generation of biodiversity in Archaea and furthers our understanding of speciation across the tree of life.

A novel acidiphilic, hydrogenotrophic methanogen, designated strain 6A8^T, was isolated from an acidic (pH 4.0–4.5) and ombrotrophic (rain-fed) bog located near Ithaca, NY, USA. Cultures were dimorphic, containing thin rods (0.2–0.3 μm in diameter and 0.8–3.0 μm long) and irregular cocci (0.2–0.8 μm in diameter). The culture utilized H₂/CO₂ to produce methane but did not utilize formate, acetate, methanol, ethanol, 2-propanol, butanol or trimethylamine. Optimal growth conditions were near pH 5.1 and 35 °C. The culture grew in basal medium containing as little as 0.43 mM Na⁺ and growth was inhibited completely by 50 mM NaCl. To our knowledge, strain 6A8^T is one of the most acidiphilic (lowest pH optimum) and salt-sensitive methanogens in pure culture. Acetate, coenzyme M, vitamins and yeast extract were required for growth. It is proposed that a new genus and species be established for this organism, Methanoregula boonei gen. nov., sp. nov. The type strain of Methanoregula boonei is 6A8^T (=DSM 21154^T =JCM 14090^T).