Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function

Abstract

Nano-sized and filterable microorganisms are thought to represent the smallest living organisms on earth and are characterized by their small size (50–400 nm) and their ability to physically pass through <0.45 μm pore size filters. They appear to be ubiquitous in the biosphere and are present at high abundance across a diverse range of habitats including oceans, rivers, soils, and subterranean bedrock. Small-sized organisms are detected by culture-independent and culture-dependent approaches, with most remaining uncultured and uncharacterized at both metabolic and taxonomic levels. Consequently, their significance in ecological roles remain largely unknown. Successful isolation, however, has been achieved for some species (e.g., Nanoarchaeum equitans and “Candidatus Pelagibacter ubique”). In many instances, small-sized organisms exhibit a significant genome reduction and loss of essential metabolic pathways required for a free-living lifestyle, making their survival reliant on other microbial community members. In these cases, the nano-sized prokaryotes can only be co-cultured with their ‘hosts.’ This paper analyses the recent data on small-sized microorganisms in the context of their taxonomic diversity and potential functions in the environment.

Nutrient enrichment induces a shift in dissolved organic carbon (DOC) metabolism in oligotrophic freshwater sediments

“…This is supported by the near-linear rate of 14 CO 2 accumulation over 7 d despite most of the 14 C being depleted from the sediment pore water very quickly (within 6 h). There were no detectable differences in cumulative 14 the glucose + N treatment, it is possible that P then became the growth-limiting nutrient, which could explain why despite the initial rapid uptake of glucose in the N addition treatment, overall C mineralisation to CO 2 was lower than for the other treatments. The addition of P alongside a C source has previously been observed to have no effect on or to even suppress C uptake in lowland agricultural soils, which has been attributed to a lack of P limitation and changes in soil chemistry, making conditions unfavourable to soil biota…”

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

“…Though not the same, ultramicrocells also exist, which are microbes with reduced cellular size due to dormancy as may be induced for various reasons including starvation [196]. The small cell size of ultrasmall microbes is matched by small genomes that do not include non-essential DNA, resulting in reduced functional potential [197]. Many ultrasmall microbes actually do not have enough metabolic capability to survive in isolation, e.g., as due to some missing complete housekeeping biochemical pathways.…”

“…Part of bioinformatic virus detection (described in Section 3.2.3) is identifying motifs typically exhibited in viruses, including enrichment of uncharacterized genes or possession of short genes, things which ultrasmall microbes can also exhibit [197]. Ultrasmall microbes thus can be similar to viruses in their genomic properties, which can make them a challenging virome contaminant to remove.…”

Diversion and phylogenetic relatedness of filterable bacteria from Norwegian tap and bottled waters

“…Given that filterable isolates represent a myriad of genera, size reduction as an adaptation to environmental stress or other factors is probably common in the bacterial world. The topic is well-surveyed in the review articles of Duda et al (2012) and Ghuneim et al (2018).…”