TY - JOUR

T1 - Diversity at low abundance

T2 - The phenomenon of the rare bacterial biosphere

AU - Skopina, M. Yu

AU - Vasileva, A. A.

AU - Pershina, E. V.

AU - Pinevich, A. V.

N1 - Publisher Copyright: © 2016, Pleiades Publishing, Ltd. Copyright: Copyright 2018 Elsevier B.V., All rights reserved.

PY - 2016/5/1

Y1 - 2016/5/1

N2 - Rare bacterial biosphere (RBB) is a large and probably predominant sector of bacterial diversity, which is specifically represented by small populations. Although some RBB components have been characterized phenotypically (actualistic objects), it has been mainly described as a set of virtual objects, i.e., of the 16S rRNA gene sequences from environmental DNA samples, which are grouped into phylotypes (operational taxonomic units, OTUs). The upper OTU threshold for RBB is presently not standardized. It is usually ~1% of the sum of OTU sequences in the metagenome library, or five sequences per OTU in absolute values. The analyzed RBB objects include (1) virtual and actualistic objects; (2) autochthonous and allochthonous forms; (3) vegetative and differentiated cells; (4) dead bacteria and free DNA; and (5) artifacts and informational gaps. The RBB phenomenon has not been sufficiently explained. According to some concepts, the RBB objects are rare due to restrictive action of unfavorable environmental factors. According to others, they utilize a successful adaptive strategy of low abundance, which facilitates higher genetic diversity, dispersal and colonization of new niches, and microbial conversion of specific substrates. Since RBB was revealed only in the early 2000s and is still poorly studied, its role in organic evolution and its place in the ecosystems should be determined by future research. The information on the RBB composition, distribution, and functions will be important for bacteriology, while some cultured species may be of basic or applied importance.

AB - Rare bacterial biosphere (RBB) is a large and probably predominant sector of bacterial diversity, which is specifically represented by small populations. Although some RBB components have been characterized phenotypically (actualistic objects), it has been mainly described as a set of virtual objects, i.e., of the 16S rRNA gene sequences from environmental DNA samples, which are grouped into phylotypes (operational taxonomic units, OTUs). The upper OTU threshold for RBB is presently not standardized. It is usually ~1% of the sum of OTU sequences in the metagenome library, or five sequences per OTU in absolute values. The analyzed RBB objects include (1) virtual and actualistic objects; (2) autochthonous and allochthonous forms; (3) vegetative and differentiated cells; (4) dead bacteria and free DNA; and (5) artifacts and informational gaps. The RBB phenomenon has not been sufficiently explained. According to some concepts, the RBB objects are rare due to restrictive action of unfavorable environmental factors. According to others, they utilize a successful adaptive strategy of low abundance, which facilitates higher genetic diversity, dispersal and colonization of new niches, and microbial conversion of specific substrates. Since RBB was revealed only in the early 2000s and is still poorly studied, its role in organic evolution and its place in the ecosystems should be determined by future research. The information on the RBB composition, distribution, and functions will be important for bacteriology, while some cultured species may be of basic or applied importance.

KW - разнообразие бактерий

KW - rare bacterial biosphere

KW - разреженная бактериальная биосфера

KW - природная ДНК

KW - высокопроизводительное секвенирование гена 16S рРНК

KW - метагеномика

KW - филотип

KW - операционная таксономическая единица

KW - эндемик.

UR - http://www.scopus.com/inward/record.url?scp=84975521013&partnerID=8YFLogxK

U2 - 10.1134/S0026261716030139

DO - 10.1134/S0026261716030139

M3 - Review article

VL - 85

SP - 272

EP - 282

JO - МИКРОБИОЛОГИЯ

JF - МИКРОБИОЛОГИЯ

SN - 0026-3656

IS - 3

ER -