BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea

Abstract

The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

A metatranscriptomics‐based assessment of small‐scale mixing of sulfidic and oxic waters on redoxcline prokaryotic communities

“…Gene predictions using the manually extended Baltic Sea reference metagenome assembly (BARM assembly, Alneberg et al ., , see details for the manual extension in the method section) were based on the mapping of 0.6–3.3 million reads per replicate (33%–47% of all protein coding reads, Supporting Information Table S1). Overall transcriptional patterns based on functional and taxonomic information revealed similar transcript composition in S and M, in which replicate samples clustered together (Supporting Information Fig.…”

“…Gene predictions using the manually extended Baltic Sea reference metagenome assembly (BARM assembly, Alneberg et al, 2018, see details for the manual extension in the method section) were based on the mapping of 0.6-3.3 million reads per replicate (33%-47% of all protein coding reads, Supporting Information Table S1). Fig.…”

“…Metagenome data were assembled using the metagenomes obtained in this study and several additional metagenomes obtained from other Baltic Sea sites and joined into the publically available Baltic Sea reference metagenome (BARM assembly, Alneberg et al, 2018). The BARM assembly was manually extended with publicly available genomic material from Sulfurimonas, SUP05 and Nitrosopumilus (Supporting Information Table S12) to improve mapping efficiency for the key taxa.…”

Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

“…Metagenomes from the 30 transect samples were included from a previous study 35 . Briefly, water from three different depth layers across the Baltic Sea was retrieved using a compact CTD profiling instrument (HYDRO-BIOS, Kiel, Germany) and samples for DNA analysis were captured on 0.2 μm pore size filters (GVWP04700, Merck Millipore, Darmstadt, Germany) and DNA extracted and stored in -80°C until further processing.…”

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change

“…surface waters and the oxic‐anoxic interfaces of the deep basins (Labrenz et al ., ; Grote et al ., ; Farnelid et al ., ), has made substantial progress in recent years. Recently, metagenomes from a time‐series of sampling station in the central BS and cruises across the various basins were successfully assembled and used to establish a reference database (BARM – Baltic reference metagenome) (Alneberg et al ., ), enabling analysis of any BS metagenome ‐ or transcriptome sample by mapping the sequences onto the database and deducing the functional and/or taxonomic profile of the community. The advantage of specific reference database was demonstrated by a recent study showing that microbial communities in the Baltic Sea, one of world's largest brackish water bodies, represent clades not previously sequenced for other freshwater or marine environments (Hugherth et al ., ).…”