We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.

Microbial metabolism upholds a fundamental role in the sustainability of water ecosystems. However, how microorganisms surviving in low-concentration substrate water environments, including the existence of emerging compounds of interest, remains unclear. In this review, microbial strategies for concentrating, utilizing, and metabolizing of low concentration substrates were summarized. Microorganisms develop substrate-concentrating strategies at both the cell and aggregate levels in substrate-limited settings. Following, microbial uptake and transport of low-concentration substrates are facilitated by adjusting physiological characteristics and shifting substrate affinities. Finally, metabolic pathways, such as mixed-substrate utilization, syntrophic metabolism, dynamic response to nutrient variation, and population density-based mechanisms allow microorganisms to efficiently utilize low-concentration substrates and to adapt to challenging oligotrophic environments. All these microbial strategies will underpin devising new approaches to tackle environmental challenges and drive the sustainability of water ecosystems, particularly in managing low-concentration contaminants (i.e., micropollutants).

Culture-independent, molecular techniques were applied to the characterization of microbial communities of an anaerobic granular sludge obtained from a full-scale digester. Procedures were optimised for total DNA recovery and polymerase chain reaction (PCR) amplification of 16S rDNA using archaea- and eubacteria-specific oligonucleotide primers. Cloned PCR products were subsequently screened by amplified rDNA restriction analysis to identify operational taxonomic units (OTUs). Inserts from clones representing each OTU were sequenced and phylogenetic trees were prepared. In addition, the microbial communities were characterised using terminal restriction fragment length polymorphism (T-RFLP). The specific methanogenic activity of the biomass, against various substrates, was also ascertained. Two anaerobic bioreactors were seeded with granular and non-granular (i.e. crushed) aliquots of the characterised sludge, respectively, and used to investigate the treatment of a volatile fatty acid (VFA)-based synthetic wastewater, at a loading rate of 5 kg COD m(-3) day(-1) at low ambient temperatures (18 degrees C). DNA was isolated from sludge samples during the test period and shifts in archaeal and eubacterial population structures were elucidated. The start-up period was successful with methane yields and COD removal efficiencies of 60-75% and 65-85%, respectively. Specific methanogenic activities of reactor biomass, obtained at the conclusion of the trial, indicated the development of psychrotolerant biomass during the 90-day experiment. Furthermore, the efficacy of T-RFLP as a molecular tool for use in the surveyance of engineered ecosystems was confirmed.