Microbial Speciation Research Articles

A Potential Case of Reinforcement in a Facultatively Sexual Unicellular Eukaryote.

The origin of a new species requires a mechanism to prevent divergent populations from interbreeding. In the classic allopatric model, divided populations evolve independently and accumulate genetic differences. If contact is restored, hybrids suffer reduced fitness and selection may favor traits that prevent mistakes in mating, a process known as reinforcement. This decisive but transient phase is challenging to document and has been reported mostly in macroorganisms. Very little is known about the processes through which new microbial species originate. In particular, it is unclear whether microbial eukaryotes, many of which can reproduce sexually during complex life cycles, speciate in much the same way as do well-studied plants and animals. Using individual cellular mate choice trials, we investigated the mating behavior of sympatric and allopatric woodland populations of the yeast Saccharomyces paradoxus. We find evidence consistent with reinforcement, potentially representing an example of microbial speciation in progress.

Investigating the effect of acid stress on selected mesophilic micro-organisms implicated in bioleaching

During start-up of heap bioleaching, low grade ores may be treated with acid for agglomeration and to combat the acid neutralising capacity of the gangue minerals. This may stress the bioleaching inocula, particularly upon inoculation during ore agglomeration. Acid addition for agglomeration varies across operations, ore types and their neutralising capacity, with limited information published on recommended concentrations. The initial pH in the agglomeration mix is typically below pH 1.0 and may be as low as pH 0.5.This paper investigates the effect of acid stress in terms of initial acid concentration and duration of exposure in submerged culture on mesophilic micro-organisms typically implicated in mineral sulphide bioleaching and critical for heap colonisation at start-up. Following acid stress, cultures were returned to standard operating conditions in batch stirred slurry reactors and their performance assessed in terms of mineral leach rates, ferrous oxidation and the rate of microbial growth. Increasing acid stress resulted in an increase in the lag period before onset of microbial growth and iron oxidation due to decreased viable cell numbers, specific metabolic activity or both. Following adaptation, typical growth and ferrous iron oxidation rates were observed under low stress conditions while reduction in the rate and extent of microbial growth and ferrous iron oxidation persisted at extreme conditions. A reduction in yield (microbial cells produced per kg iron oxidised) was observed with increased acid concentration over comparative times. Microbial speciation analysis indicated a substantial decrease in the diversity of the microbial species surviving.

Population genetic analysis of Streptomyces albidoflavus reveals habitat barriers to homologous recombination in the diversification of streptomycetes.

Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes.

Strain-level genomic variation in natural populations ofLebetimonasfrom an erupting deep-sea volcano

Chemolithoautotrophic Epsilonproteobacteria are ubiquitous in sulfidic, oxygen-poor habitats, including hydrothermal vents, marine oxygen minimum zones, marine sediments and sulfidic caves and have a significant role in cycling carbon, hydrogen, nitrogen and sulfur in these environments. The isolation of diverse strains of Epsilonproteobacteria and the sequencing of their genomes have revealed that this group has the metabolic potential to occupy a wide range of niches, particularly at dynamic deep-sea hydrothermal vents. We expand on this body of work by examining the population genomics of six strains of Lebetimonas, a vent-endemic, thermophilic, hydrogen-oxidizing Epsilonproteobacterium, from a single seamount in the Mariana Arc. Using Lebetimonas as a model for anaerobic, moderately thermophilic organisms in the warm, anoxic subseafloor environment, we show that genomic content is highly conserved and that recombination is limited between closely related strains. The Lebetimonas genomes are shaped by mobile genetic elements and gene loss as well as the acquisition of novel functional genes by horizontal gene transfer, which provide the potential for adaptation and microbial speciation in the deep sea. In addition, these Lebetimonas genomes contain two operons of nitrogenase genes with different evolutionary origins. Lebetimonas expressed nifH during growth with nitrogen gas as the sole nitrogen source, thus providing the first evidence of nitrogen fixation in any Epsilonproteobacteria from deep-sea hydrothermal vents. In this study, we provide a comparative overview of the genomic potential within the Nautiliaceae as well as among more distantly related hydrothermal vent Epsilonproteobacteria to broaden our understanding of microbial adaptation and diversity in the deep sea.

Role and characteristics of problematic biofilms within the removal and mobility of trace metals in a pilot-scale membrane bioreactor

The characteristics of problematic biofilms (i.e., fouling and clogging layers) were studied with regards to the removal and fate of trace metals (contents well under 100μg/L) during the long-term operation of a pilot-scale membrane bioreactor for the treatment of real wastewaters from a large industrial area.Results showed that clogging layer was more effective than suspended activated sludge in the biosorption of As>Zn>Ni>Cd>Sb>Fe>Se due to the synergic effects of extracellular polymeric compounds and metal-resistant bacteria. In fact the selective microbial speciation of the phylum of Bacteroidetes, which is highly resistant to heavy metals, was observed in the clogging sludge in spite of the very low concentration of dissolved metals in the bioreactor.Compared to the suspended activated sludge, the clogging layer enhanced the biosorption of very toxic substances such as As, Cd and Ni. In fact, the metal contents were respectively: 7.9–7.4 vs. 690–840μgAs/kgTS; 1.5–2.2 vs. 149–219μgCd/kgTS; 58.8–71.7 vs. 227–298μgNi/kgTS. Then, the potential desorption of metals during the membrane acid cleanings was estimated as relevant as 10–15% of the metals associated to the clogging sludge. The combined effects of pH and the selected microbial community, and the minor effect of the redox potential, let us conclude on the major importance of bio-sorption/desorption mechanisms with respect to bio-precipitation/dissolution.

What can genome-scale metabolic network reconstructions do for prokaryotic systematics?

It has recently been proposed that in addition to Nomenclature, Classification and Identification, Comprehending Microbial Diversity may be considered as the fourth tenet of microbial systematics [Staley JT (2010) The Bulletin of BISMiS, 1(1): 1-5]. As this fourth goal implies a fundamental understanding of microbial speciation, this perspective article argues that translation of bacterial genome sequences into metabolic features may contribute to the development of modern polyphasic taxonomic approaches. Genome-scale metabolic network reconstructions (GSMRs), which are the result of computationally predicted and experimentally confirmed stoichiometric matrices incorporating all enzyme and metabolite components encoded by a genome sequence, provide a platform that can illustrate bacterial speciation. As the topology and the composition of GSMRs are expected to be the result of adaptive evolution, the features of these networks may provide the prokaryotic taxonomist with novel tools for reaching the fourth tenet of microbial systematics. Through selected examples from the Actinobacteria, which have been inferred from GSMRs and experimentally confirmed after phenotypic characterisation, it will be shown that this level of information can be incorporated into modern polyphasic taxonomic approaches. In conclusion, three specific examples are illustrated to show how GSMRs will revolutionize prokaryotic systematics, as has previously occurred in many other fields of microbiology.

The effect of UV pre-treatment on biofouling of BWRO membranes: A field study

The use of biocides, particularly chlorine, in reverse osmosis (RO) desalination is widely practiced despite documented evidence that although biocides may be advantageous in controlling microbial counts in the water, in some cases they can actually exacerbate biofouling of the membranes. The adverse effects, associated with widespread biocide use, have spurred the need for finding alternative RO pre-treatment disinfection methods. Ultraviolet (UV) disinfection, and specifically medium pressure ultraviolet (MP-UV) disinfection has been considered a possible alternative and is now gaining recognition as a viable disinfection method applicable to RO desalination; however documentation on the effects of UV pre-treatment on RO membrane biofouling is scarce. This paper reports the findings from a four month field study conducted at a brackish water reverse osmosis (BWRO) desalination plant, treating groundwater, in the north of Israel, in which MP-UV was applied as a pre-treatment disinfection step prior to RO desalination. The plant contains two double stage desalination trains that operate in parallel — one train served as a reference, while in the other an Atlantium HOD™MP-UV system was installed. Both trains were run in parallel, and for the duration of the study, all normalized performance parameters were collected and microbial counts monitored. At the end of the run previously replaced sacrificial membranes, situated in the front of the first stages, were autopsied and various biofilm analyses were conducted to elucidate cell/extracellular polymeric substances (EPS) content and microbial speciation. The overall results suggest that MP-UV pre-treatment prolonged the train performance, which manifested itself in a lower relative normalized permeate flux decline vs. the train which received water without MP-UV pre-treatment (11% vs. 17%, respectively). Significantly less EPS was found on the RO membrane which received MP-UV treated water. The differences in biofilm thickness and cell density counts (cells/cm2) between the two membranes were notable, in favor of UV pre-treatment, yet less significant. The MP-UV pre-treatment also had a substantial effect on biofilm community composition; the RO membrane that received MP-UV disinfected water exhibited a biofilm in which the diversity was reduced by 30% and more, and did not contain certain phylogenetic groups that were detected on the RO membrane that received water without MP-UV pre-treatment. It can be concluded that pre-treatment disinfection using MP-UV may be a promising option for combating biofouling of RO membranes and prolonging operation of the trains between cleaning regimes.

A Model for the Effect of Homologous Recombination on Microbial Diversification

The effect of homologous recombination (HR) on the evolution of microbial genomes remains contentious as competing hypotheses seek to explain the evolutionary dynamics of microbial species. Evidence for HR between microbial genomes is widespread, and this process has been proposed to act as a cohesive force that can constrain the diversification of microbial lineages. We seek to characterize the evolutionary dynamics of sympatric populations to explore the impact of HR on microbial speciation. We describe a simple equation for quantifying the cohesive effect of HR on microbial populations as a function of their nucleotide divergence, μ/ρ = πg10 − 20 πg. The model was verified using a forward-time microbial population simulator that can explore the evolutionary dynamics of sympatric populations in nonoverlapping niche space. The model was also evaluated using multilocus sequence data from a range of microbial species, providing criteria for dividing them into either cohesively recombining or clonally diverging lineages. We conclude that models of microbial diversification that appear contradictory can be explained in a unified manner as the natural and predictable consequence of variation in a small number of population parameters.

Effect of aspartate and glutamate on the fate of enhanced biological phosphorus removal process and microbial community structure

This study investigated the fate of enhanced biological phosphorus removal (EBPR) and changes in microbial speciation in a sequencing batch reactor (SBR) fed with aspartate and glutamate. It involved SBR operation for 288 days, batch tests for observation of metabolic functions together with microscopic and phylogenetic analyses. Polyphosphate accumulating organisms (PAOs) were observed in abundance with complete removal of phosphorus. Fluorescence in situ hybridization (FISH) combined with 4',6-dia-midino-2-phenylindole (DAPI) staining confirmed the accumulation of polyphosphate by Rhodocyclus-related and Actinobacterial PAOs. Aspartate seemed to favor the competitive growth of Rhodocyclus-related PAOs since EBPR population used the common biochemical pathways followed by Rhodocyclus-related PAOs in the aspartate fed batch tests. In the glutamate fed batch reactors, however, Actinobacterial PAOs appeared to be competitively selected which explains the lower levels of PHA generation. Even though operational conditions did not change, effective EBPR could not be maintained during the latter part of the study.

Limits to gene flow in a cosmopolitan marine planktonic diatom

The role of geographic isolation in marine microbial speciation is hotly debated because of the high dispersal potential and large population sizes of planktonic microorganisms and the apparent lack of strong dispersal barriers in the open sea. Here, we show that gene flow between distant populations of the globally distributed, bloom-forming diatom species Pseudo-nitzschia pungens (clade I) is limited and follows a strong isolation by distance pattern. Furthermore, phylogenetic analysis implies that under appropriate geographic and environmental circumstances, like the pronounced climatic changes in the Pleistocene, population structuring may lead to speciation and hence may play an important role in diversification of marine planktonic microorganisms. A better understanding of the factors that control population structuring is thus essential to reveal the role of allopatric speciation in marine microorganisms.

Meeting on the Microbiology of Soils, Autumn 2001

Records of the testate amoeba fauna of soils have accumulated throughout the 20 t h century from numerous sites on all the Earth's continents, ranging from equatorial to polar, with analyses of species assemblages in relation to environmental conditions - especially hydrological. Testates have considerable potential to be used as indicators of environmental change and to give insight into the processes of microbial biogeography and speciation. Small ubiquitous species may have an essential role in the biological succcession as soils develop from mineral substrates. Present knowledge suggests that future research in these areas will be of high value.

Meeting on the Microbiology of Soils, Autumn 2001Testate amoebae – past, present and future

Records of the testate amoeba fauna of soils have accumulated throughout the 20 th century from numerous sites on all the Earth's continents, ranging from equatorial to polar, with analyses of species assemblages in relation to environmental conditions – especially hydrological. Testates have considerable potential to be used as indicators of environmental change and to give insight into the processes of microbial biogeography and speciation. Small ubiquitous species may have an essential role in the biological succcession as soils develop from mineral substrates. Present knowledge suggests that future research in these areas will be of high value.