Diversity at low abundance: The phenomenon of the rare bacterial biosphere

Abstract

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 usuallỹ 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.

Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert

“…The principle objectives of this study were to determine how diverse actinobacterial communities are in the Atacama Desert and how big a resource this presents for biotechnology exploitation, and to dissect such diversity in terms of actinobacterial rare and previously undetected dark matter 21 , 22 . To this end, we have applied R H Whittaker’s classic diversity indices 23 to actinobacterial diversity of a hyper-arid—extreme hyper-arid landscape at five distinct habitats covering an altitude range of approximately 900–2500 m absl.…”

The Pelagic Bacterium Paraphotobacterium marinum Has the Smallest Complete Genome Within the Family Vibrionaceae

“…The seven sequences were classified into a single OTU (denovo_289). The low relative abundance of P. marinum indicated that it was a rare bacterial species which were regarded as the threshold of five sequences per OTU ( Skopina et al, 2016 ). Thus, it is assumed that P. marinum is present as a rare species in the surface seawater.…”

Contrasting Patterns of the Bacterial Communities in Melting Ponds and Periglacial Rivers of the Zhuxi glacier in the Tibet Plateau

“…An important trait of the rare biosphere is the extremely high diversity, which facilitates their contributions to the entire communities [57] and has been termed the "seed bank" effect [24,25]. Within melt ponds and periglacial rivers, rare sub-communities were significantly more diverse than the dominant sub-communities.…”

“…Although it has long been known that bacterial species interact with each other to form complicated networks capable of community level functions, such interaction in glacial ecosystems have only been studied very recently [22,23]. Furthermore, modern ecology has recognized the over-proportional role of rare species, especially in pristine environments [24,25]. For instance, it is the rare biosphere that controls the succession strategy and ecological functions of bacterial communities during early periglacial lake ontogeny [26].…”