Size Matters: Ultra-small and Filterable Microorganisms in the Environment

Abstract

Ultra-small microorganisms are ubiquitous in Earth's environments. Ultramicrobacteria, which are defined as having a cell volume of <0.1 μm³, are often numerically dominant in aqueous environments. Cultivated representatives among these bacteria, such as members of the marine SAR11 clade (e.g., "Candidatus Pelagibacter ubique") and freshwater Actinobacteria and Betaproteobacteria, possess highly streamlined, small genomes and unique ecophysiological traits. Many ultramicrobacteria may pass through a 0.2-μm-pore-sized filter, which is commonly used for filter sterilization in various fields and processes. Cultivation efforts focusing on filterable small microorganisms revealed that filtered fractions contained not only ultramicrocells (i.e., miniaturized cells because of external factors) and ultramicrobacteria, but also slender filamentous bacteria sometimes with pleomorphic cells, including a special reference to members of Oligoflexia, the eighth class of the phylum Proteobacteria. Furthermore, the advent of culture-independent "omics" approaches to filterable microorganisms yielded the existence of candidate phyla radiation (CPR) bacteria (also referred to as "Ca. Patescibacteria") and ultra-small members of DPANN (an acronym of the names of the first phyla included in this superphyla) archaea. Notably, certain groups in CPR and DPANN are predicted to have minimal or few biosynthetic capacities, as reflected by their extremely small genome sizes, or possess no known function. Therefore, filtered fractions contain a greater variety and complexity of microorganisms than previously expected. This review summarizes the broad diversity of overlooked filterable agents remaining in "sterile" (<0.2-μm filtered) environmental samples.

Keywords: candidate phyla radiation; filterable microorganisms; minimal cell; ultramicrobacteria; ultramicrocells.

Fig. 1.

Diagram showing filterable microorganisms in the environment. (I) ultramicrocells; (II) obligate ultramicrobacteria; (III) facultative ultramicrobacteria; (IV) slender filamentous bacteria; (V) ultra-small members of CPR bacteria (also referred to as “Candidatus Patescibacteria”) and DPANN archaea indicated by the arrow in this Figure. See details in the text. This figure was created with BioRender (https://biorender.com/).

Fig. 2.

Scanning electron micrograph of c-shaped cells of Aurantimicrobium minutum KNC^T. Cells were cultured in organic NSY (nutrient broth, soytone, and yeast extract; Hahn et al., 2004) medium for two weeks. Scale bar: 200 nm. This micrograph is an unpublished figure from the author; other micrographs of this species are shown in Nakai et al. (2013, 2015).

Fig. 3.

Micrograph of pleomorphic cells of Oligoflexus tunisiensis Shr3^T. Cells were cultured in R2A medium for more than two weeks. This micrograph is slightly modified from the figure originally published in Nakai and Naganuma (2015). Scale bar: 10 μm.

Fig. 4.

A schematic diagram of the “middle-out” approach toward the development of minimal cells or synthetic cells. This approach, inspired by the unusual biology of ultra-small life forms, may provide a new perspective to traditional top-down or bottom-up approaches. This figure was created with BioRender (https://biorender.com/).