Freshwater bacterial lifestyles inferred from comparative genomics

While micro‐organisms actively mediate and participate in freshwater ecosystem services, we know little about freshwater microbial genetic diversity. Genome sequences are available for many bacteria from the human microbiome and the ocean (over 800 and 200, respectively), but only two freshwater genomes are currently available: the streamlined genomes of Polynucleobacter necessarius ssp. asymbioticus and the Actinobacterium AcI‐B1. Here, we sequenced and analysed draft genomes of eight phylogentically diverse freshwater bacteria exhibiting a range of lifestyle characteristics. Comparative genomics of these bacteria reveals putative freshwater bacterial lifestyles based on differences in predicted growth rate, capability to respond to environmental stimuli and diversity of useable carbon substrates. Our conceptual model based on these genomic characteristics provides a foundation on which further ecophysiological and genomic studies can be built. In addition, these genomes greatly expand the diversity of existing genomic context for future studies on the ecology and genetics of freshwater bacteria.     

The beta-lactamase threat in Enterobacteriaceae, Pseudomonas and Acinetobacter

Over the past 60 years, the use of successive generations of beta-lactam antibiotics has selected successive generations of beta-lactamase enzymes, each more potent than the last. Currently, rising problems include CTX-M extended-spectrum beta-lactamases (ESBLs), plasmid-mediated AmpC beta-lactamases and KPC carbapenemases in Enterobacteriaceae, while OXA- and metallo- carbapenemases are of growing importance in Acinetobacter spp. and (less so) in other non-fermenters. Escherichia coli isolates with CTX-M ESBLs are spreading multiresistance in the community and in hospitals, while carbapenemase-producing Acinetobacter spp., mostly from intensive care, are among the most multiresistant nosocomial bacteria known and are often susceptible only to polymyxins and, potentially, tigecycline. This review discusses the epidemiology and microbiology of these resistance problems, along with possible solutions.     

The role of ISAba1 in expression of OXA carbapenemase genes in Acinetobacter baumannii

ISAba1 was found in all widespread clones of Acinetobacter baumannii in the United Kingdom. All isolates studied had a blaOXA-51-like carbapenemase gene; some also had blaOXA-23-like and/or blaOXA-58-like. Among isolates with blaOXA-51-like as sole carbapenemase gene, only those with ISAba1 adjacent to blaOXA-51-like were carbapenem resistant. Minor differences in blaOXA-51-like sequence were observed in resistant and susceptible isolates. Isolates with blaOXA-23-like in addition were consistently resistant to carbapenems; in all of these ISAba1 lay upstream of blaOXA-23-like, but was not associated with blaOXA-51-like. These results suggest that ISAba1 is providing the promoter for blaOXA-51-like and, probably, for blaOXA-23-like.     

Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high‐throughput sequencing sets

Fungi are everywhere and interact with humans in countless ways, but a large group of fungi called ‘Cryptomycota’ has escaped detection until very recently. Still, the extent of diversity and ecological habits of this group remain largely unknown. We interrogated publically available 18S rRNA gene datasets, obtained via high‐throughput sequencing from marine and freshwater samples, for Cryptomycota sequences. Contrary to previous work, we found evidence of substantial Cryptomycota diversity in the marine upper water column. Additionally, we produced a sequencing set from a groundwater aquifer, an environment unrepresented among 18S rRNA gene pyrosequencing sets. The Cryptomycota community in this aquifer sample appears distinct from the community in both freshwater and marine environments with evidence of a unique aquifer clade. This study significantly expands the boundary of known Cryptomycota sequence diversity and characterizes the phylogenetic distribution of this diversity in aquatic environments. Furthermore, the approach utilized is generalizable to discovery of novel micro‐eukaryotic diversity from any lineage.     

Local–global overlap in diversity informs mechanisms of bacterial biogeography

Spatial variation in environmental conditions and barriers to organism movement are thought to be important factors for generating endemic species, thus enhancing global diversity. Recent microbial ecology research suggested that the entire diversity of bacteria in the global oceans could be recovered at a single site, thus inferring a lack of bacterial endemism. We argue this is not the case in the global ocean, but might be in other bacterial ecosystems with higher dispersal rates and lower global diversity, like the human gut. We quantified the degree to which local and global bacterial diversity overlap in a diverse set of ecosystems. Upon comparison of observed local–global diversity overlap with predictions from a neutral biogeography model, human-associated microbiomes (gut, skin, mouth) behaved much closer to neutral expectations whereas soil, lake and marine communities deviated strongly from the neutral expectations. This is likely a result of differences in dispersal rate among ‘patches'', global diversity of these systems, and local densities of bacterial cells. It appears that overlap of local and global bacterial diversity is surprisingly large (but likely not one-hundred percent), and most importantly this overlap appears to be predictable based upon traditional biogeographic parameters like community size, global diversity, inter-patch environmental heterogeneity and patch connectivity.