Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River

Abstract

River water is a small percentage of the total freshwater on Earth but represents an essential resource for mankind. Microbes in rivers perform essential ecosystem roles including the mineralization of significant quantities of organic matter originating from terrestrial habitats. The Amazon river in particular is famous for its size and importance in the mobilization of both water and carbon out of its enormous basin. Here we present the first metagenomic study on the microbiota of this river. It presents many features in common with the other freshwater metagenome available (Lake Gatun in Panama) and much less similarity with marine samples. Among the microbial taxa found, the cosmopolitan freshwater acI lineage of the actinobacteria was clearly dominant. Group I Crenarchaea and the freshwater sister group of the marine SAR11 clade, LD12, were found alongside more exclusive and well known freshwater taxa such as Polynucleobacter. A metabolism-centric analysis revealed a disproportionate representation of pathways involved in heterotrophic carbon processing, as compared to those found in marine samples. In particular, these river microbes appear to be specialized in taking up and mineralizing allochthonous carbon derived from plant material.

Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River

“…The presence of amoABC genes in these data (Ghai et al, 2011) raises the question of whether chemoautotrophic ammonia oxidation might also be occurring in the lower Amazon reaches. Other freshwater habitats have been found to host Thaumarchaeota cells in the water column, including lakes and rivers (Urbach et al, 2001;Lehours et al, 2007;Auguet et al, 2011;Liu et al, 2011), where they can account for up to 47% of prokaryotic cells (Callieri et al, 2009).…”

“…Evidence of Archaea belonging to the phylum Thaumarchaeota has recently been found in metagenomic libraries of the upper reaches of Amazon River system (Ghai et al, 2011;Santos-Júnior et al, 2017). The presence of amoABC genes in these data (Ghai et al, 2011) raises the question of whether chemoautotrophic ammonia oxidation might also be occurring in the lower Amazon reaches.…”

“…Metagenomicand metatranscriptomic-based gene and transcript inventories in freshwater environments have provided insights into the functions of these microbes (Rusch et al, 2007;Pope and Patel, 2008;Debroas et al, 2009;Ghai et al, 2011;Oh et al, 2011;VilaCosta et al, 2013;Quaiser et al, 2014;Tsementzi et al, 2014). When normalized with internal standards Satinsky et al, 2013), metagenomic and metatranscriptomic datasets collected in parallel can be used to calculate expression levels for each gene (transcripts gene copy −1 ).…”

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

“…Ghai et al analyzed metagenomic data from lakes, estuaries (Ghai et al, 2012), and rivers (Ghai et al, 2011), and found that acI members have a lower than expected GC genomic content. Martinez-Garcia et al (2012) used single-cell genomics and found that the origins of more than 80% of rhodopsins found among lake bacteria belong to the actinobacteria.…”

Considerations for the development and application of control materials to improve metagenomic microbial community profiling

“…The term environment in this context refers not only to the classic outdoor terrestrial [1] and aquatic [2,3] domains, but also environments found within other organisms, like the gut [4,5] and associated matrices like probiotic supplements [6] or linked to other man-made scenarios like water purification [7] or during fermentation [8]. The field of metagenome analysis (metagenomics) has grown rapidly as the last 10 years have seen the development and establishment of next generation (also termed massively parallel) sequencing (NGS), a technique that has the potential to read over a billion sequences in a single run.…”