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This new study, by ENIGMA researchers, examined the newly-defined superphylum Patescibacteria, finding that they have developed unique characteristics which help adapt themselves to nutrient-limited but stable conditions in groundwater. Characteristics include highly reduced genome sizes and ultra-small cell size with simplified metabolism pathways for energy and carbon utilization as well as basic systems for DNA replication and translation essential for growth and reproduction. Meanwhile, they lack numerous nonessential functions related to motility, chemotaxis, outer membrane function, polysaccharide metabolism, etc. They also lack CRISPR-mediated phage defense, considered the most important mechanism of bacterial immunity; while possessing alternative strategies for phage resistance.
Groundwater microbial communities are responsible for large-scale subsurface biogeochemical cycling, influencing the chemical profiles of the world’s water. Patescibacteria is found prevalent in groundwater, sediment, lake, and other aquifer environments. It has been observed that bacteria from this superphylum have extremely small genome sizes and cell sizes, and they lack the CRISPR virus defense system. However, there is little understanding of the mechanisms used by Patescibacteria to thrive in the nutrient-limited groundwater environment. Also, their fragility to environmental stresses (such as heavy metal contamination) was not known. This study, based on previous studies and results, further explored the adaptive mechanisms of Patescibacteria comprehensively by comparing genomic features and linking them to environmental factors. We also found that Patescibacteria has a reduced stress response to environmental perturbations which might be related to its vulnerability to heavy metal contamination observed in this study. Since terrestrial subsurface aquifers are the repository of one-third of the Earth’s fresh water and an important source of water for human consumption; groundwater pollution may alter groundwater microbial communities, impacting water health. Thus, understanding the characterization of Patescibacteria is important to the conservation of groundwater.
Samples from a site exposed to radioactive contamination; targeting 93 contaminated and uncontaminated groundwater wells over time, showed that Patescibacteria superphyla is diverse and includes over 20 candidate phyla. Defined by ultra-small cell sizes, simplified membrane structures, and loss of genes, facilitating genome sizes three times smaller than other well-established bacterial phyla; retaining essential functions of simple metabolism and genetic information processing. Based on analysis of Patescibacteria, we propose that their adaptation to groundwater environments drives their unique genomic features.
Low nutrient concentration and diversity in groundwater require Patescibacteria to increase the absorption rate. Smaller cells have a higher ratio of surface area to volume, thus speeding up substance exchange rates across the cell membrane. Small cell size and reduced membrane structures, which could be potential phage receptors, allow Patescibacteria to escape from phage attachment. Groundwater has low oxygen concentrations and no light for photosynthesis. Thus, Patescibacteria relies on anaerobic respiration which provides less energy than aerobic respiration, losing genes for light capture & repair of light damage. Functions with high energy requirements such as flagellar motility and secondary metabolisms are also missing. Stable physical conditions such as temperature and pH in groundwater reduce the need for adaptive responses to environmental perturbation. Indeed, Patescibacteria abundance was significantly reduced in highly contaminated groundwater compared to uncontaminated /moderately contaminated groundwater, indicating that reduced metabolic potential and stress response make Patescibacteria sensitive to contamination.
Tian, R; D. Ning, Z. He, P. Zhang, S.J. Spencer, S. Gao, W. Shi, L. Wu, Y. Zhang, Y. Yang, B. G. Adams, A.M. Rocha, B.L. Detienne, K.A. Lowe, D.C. Joyner, D.M. Klingeman, A.P. Arkin, M.W. Fields, T.C. Hazen, D.A. Stahl, E.J. Alm, J. Zhou (2020) Small is mighty: adaptation of Patescibacteria to groundwater environment drives their genome simplicity. Microbiome. ISME Journal [doi]:1186/s40168-020-00825-w