Evolution of small prokaryotic genomes

As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria); metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature

Interactions between abundant fungal species influence the fungal community assemblage on limestone

<div><p>The assembly of fungal communities on stone materials is mainly influenced by the differential bioreceptivity of such materials and environmental conditions. However, little is known about the role of fungal interactions in the colonization and establishment of fungal species. We analyzed the effects of intra- and interspecific interactions between 11 species of fungi in oligotrophic and copiotrophic media and on limestone coupons. In a previous study, these species were the most frequently isolated in the epilithic biofilms of limestone walls exposed to a subtropical climate. In the culture media, we found a greater frequency of intra- and interspecific inhibitory effects in the oligotrophic medium than in the copiotrophic medium. On the limestone coupons, all fungi were able to establish; however, the colonization success rate varied significantly. <i>Cladosporium cladosporioides</i> had a less extensive colonization in isolation (control) than in dual interactions (coexistence) with other species. <i>Phoma eupyrena</i> exhibited the highest colonization success rate and competitive dominance among all tested species. X-ray diffraction (XRD) and scanning electron microscope (SEM) analyses revealed that <i>Pestalotiopsis maculans</i> and <i>Paraconiothyrium</i> sp. produced calcium oxalate crystals during their growth on coupon surfaces, both in isolation and in dual interactions. Our results demonstrate that interactions between abundant fungal species influence the fungal colonization on substrates, the biomineralization and the fungal community assemblage growing in limestone biofilms.</p></div

Fungal isolates used for interaction assays in culture media and on limestone coupons in addition to the number of times fungi were isolated in young (Y), middle-aged (M) and old (O) biofilms with distinct environmental exposure times [8].

<p>Fungal isolates used for interaction assays in culture media and on limestone coupons in addition to the number of times fungi were isolated in young (Y), middle-aged (M) and old (O) biofilms with distinct environmental exposure times [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188443#pone.0188443.ref008" target="_blank">8</a>].</p

SEM images of limestone coupon surfaces colonized by paired fungi after four months depicting the calcium oxalate crystals produced by some species.

<p>A) <i>C</i>. <i>cladosporioides</i>–<i>Paraconiothyrium</i> sp., B) <i>C</i>. <i>lunata</i>, C) <i>Paraconiothyrium</i> sp.–<i>P</i>. <i>eupyrena</i>, D) <i>C</i>. <i>lunata</i>–<i>P</i>. <i>maculans</i>, E) <i>Paraconiothyrium</i> sp., F) <i>M</i>. <i>roridum</i>–<i>P</i>. <i>maculans</i>, G) <i>C</i>. <i>cladosporioides</i>–<i>P</i>. <i>maculans</i>, H) <i>P</i>. <i>maculans</i>, and I) <i>P</i>. <i>maculans</i>–<i>P</i>. <i>eupyrena</i>. Black arrows indicate polymeric fungal production. Cc: Conidiophore; C: conidia; P: pycnidia.</p

Fungal interaction types, antagonism index (AI) scores and inhibition and resistance percentages per species with respect to all paired species (ten) and itself in MEAC and CACO media.

<p>The AI categories are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188443#pone.0188443.t002" target="_blank">Table 2</a>.</p

Intra- and interspecific interactions between paired fungi in culture media.

<p>Columns 1 and 3: CACO medium; columns 2 and 4: MEAC medium. A and B) <i>C</i>. <i>cladosporioides</i>–<i>P</i>. <i>maculans</i>, C and D) <i>M</i>. <i>roridum</i>–Hyphomycete sp., E and F) <i>F</i>. <i>redolens</i>–<i>C</i>. <i>clavata</i>, G and H) <i>P</i>. <i>maculans</i>–<i>P</i>. <i>eupyrena</i>, I and J) <i>S</i>. <i>constrictum</i>–<i>F</i>. <i>redolens</i>, K and L) <i>Paraconiotrhyrium</i> sp.–<i>F</i>. <i>oxysporum</i>, M and N) <i>C</i>. <i>cladosporioides</i>–<i>C</i>. <i>cladosporioides</i>, O and P) <i>P</i>. <i>eupyrena</i>–<i>C</i>. <i>lunata</i>, Q and R) <i>Paraconiothyrium</i> sp.–<i>C</i>. <i>lunata</i>, S and T) <i>M</i>. <i>roridum</i>–<i>P</i>. <i>eupyrena</i>.</p

Percentage of limestone coupon surfaces colonized by interacting fungal species after four months of exposure.

<p>Percentage of limestone coupon surfaces colonized by interacting fungal species after four months of exposure.</p

Percentage of limestone coupon surfaces colonized by fungi (controls) after four months of exposure.

<p>Percentage of limestone coupon surfaces colonized by fungi (controls) after four months of exposure.</p

Types of paired fungal interactions or reactions and corresponding values for abundant fungal species on limestone biofilms.

<p>Modified from Yuen et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188443#pone.0188443.ref031" target="_blank">31</a>].</p

Interaction between <i>Curvularia lunata</i> and <i>Phoma eupyrena</i>.

<p>A) Coupons four months after inoculation, B) microphotography of a coupon, C) surface after sampling by points, D) area colonized by <i>C</i>. <i>lunata</i> (green), <i>P</i>. <i>eupyrena</i> (grey) and both species (yellow) and area without growth (white) in triplicate limestone coupons in the CACO medium.</p