The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK.
Science (Impact Factor: 33.61). 03/2009; 323(5915):741-6. DOI: 10.1126/science.1159388
Source: PubMed


The Bacteria and Archaea are the most genetically diverse superkingdoms of life, and techniques for exploring that diversity are only just becoming widespread. Taxonomists classify these organisms into species in much the same way as they classify eukaryotes, but differences in their biology-including horizontal gene transfer between distantly related taxa and variable rates of homologous recombination-mean that we still do not understand what a bacterial species is. This is not merely a semantic question; evolutionary theory should be able to explain why species exist at all levels of the tree of life, and we need to be able to define species for practical applications in industry, agriculture, and medicine. Recent studies have emphasized the need to combine genetic diversity and distinct ecology in an attempt to define species in a coherent and convincing fashion. The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date.

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    • "Cyanobacteria are the oxygenic photosynthetic prokaryotes that appeared approximately 2.4 billion years ago [1]. These organisms possess a wide variability of physiological strategies which allow them to occupy the diverse ecological habitats in the terrestrial, fresh water and marine surroundings with the widely fluctuating environmental factors such as light intensity and quality, temperature, nutrient availability and water activity [2] [3] [4] [5] [6]. Although cyanobacteria are prokaryotic, they are similar to the plants in having chlorophyll a and the ability to perform oxygenic photosynthesis. "
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    ABSTRACT: This study was targeted to find new sources of phycobiliproteins (PBP) as these are important as natural colours, antioxidants and fluorescent markers. Here we report Anabaena fertilissima PUPCCC 410.5 as a good producer of PBP. Control cultures of the cyanobacterium produced 383 μg PBP mg −1 dry biomass on day 8. The pH of the medium , supplementation of nitrogen source, sugar and illumination of cultures with different colours of light were optimized for PBP production. Optimized individual parameters were: pH of the medium 7.5; supplementation of 2 mmol nitrite L −1 or 0.5% sucrose; and illumination of cultures with blue light. Total PBP production under these conditions ranged between 627 and 696 μg mg −1 dry biomass, resulting in nearly 1.6 fold increase, with a significant increase in phycocyanin content. Incubation of 2 mmol nitrite L −1 supplemented cultures in blue light resulted in nearly 4.5 fold increase in phycoerythrin compared to the control cultures. The PBP/phycocyanin/ phycoerythrin production under the optimized conditions by Anabaena fertilissima PUPCCC 410.5 is significantly higher than the PBP production by the other cyanobacterial strains reported in literature. Thus this cyanobacterial strain is a promising candidate for PBP production at commercial level.
    Full-text · Article · Oct 2015 · Algal Research
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    • "The urgency of this issue has been highlighted over the last decade, as advances in sequencing technology prompted a boom in the study of microbial diversity in natural environments [5] [6] [7] [8] [9] [10] [11]. In the microbial world, the partitioning problem is intensified by the prevalence of asexual reproduction and horizontal gene transfer [12] [13]. Nevertheless, the currently dominant view in the field is that the partitioned community assumption, while conceptually problematic, is operationally necessary [14] [15] [16] [17]. "
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    ABSTRACT: Most of classical theoretical ecology is based on the assumption that organisms in a community can be naturally partitioned into groups of individuals that can be treated as identical. At the same time, mounting experimental evidence from studies of microbial communities raises the intriguing question whether this intuition is an accurate description of the microbial world. This work builds on Mac Arthur's model of competitive coexistence on multiple resources to construct a framework that does not rely on postulated existence of species as fundamental ecological variables. In one parameter regime, effective "species" with a core and accessory genome naturally appear in this model as emergent concepts. However, the same model allows a smooth transition to a highly diverse regime where the species formalism becomes inadequate. An alternative description is proposed based on the dynamical modes of population fluctuations. This approach provides a naturally hierarchical description of community dynamics which is well-defined even when the species description breaks down. The relevance of this framework for understanding the complexity of naturally observed microbial communities is discussed.
    Full-text · Article · Apr 2015
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    • "Also, the genomes would be altered greatly while microbiota survive at various niches in rhizosphere. The environmental gradients in rhizosphere could maintain complex niches, where the accessory genomes of microbial strains have been altered greatly (Fraser et al. 2009). "
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    ABSTRACT: AimsThe response of microbial metagenome to polycyclic aromatic hydrocarbons (PAHs) degradation in the rice rhizosphere remains poorly understood. We investigated the spatial and temporal variations of microbial communities and reconstructed metagenomes along the rice rhizosphere gradient during PAHs degradation.Methods and ResultsThe experiment was performed in rhizoboxes, in which the rhizosphere region was divided into five 1-mm thick layers. Based on denaturant gradient gel electrophoresis profiling and sequencing of bacterial and archaeal 16S rRNA genes, predicted metagenomes were reconstructed. The microbial communities in the rice rhizosphere were influenced by the PAHs concentration and distance from the root surface during PAHs degradation. Correlation network analysis showed that archaea played an important role in PAHs degradation. Predicted metagenomes can be clustered into two groups with high and low PAHs degrading potential, respectively. The relative abundance of genes for defense mechanisms, replication, recombination and reparation was significantly higher in samples with high PAHs degrading potentials. The relative abundance of the dioxygenase gene was greater near the root surface of the rice. However, the abundance of aldolase and dehydrogenase was constant in rhizosphere soils at different distances from the root surface.Conclusions Distance from root surface and PAH concentrations affected the microbial communities and metagenomes in rice rhizosphere. The abundance of dioxygenase genes relating to PAH degradation in metagenomes mirrored the PAH degradation potential in rice rhizosphere.Significance and Impact of the StudyOur findings suggested that the predicted metagenomes reconstructed from 16S rRNA marker gene sequences provide further insights into the spatial variation and dynamics of microbial functioning that occur during bioremediation.
    Full-text · Article · Jan 2015 · Journal of Applied Microbiology
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