Structural basis for high‐affinity adipate binding to AdpC (<scp>RPA</scp>4515), an orphan periplasmic‐binding protein from the tripartite tricarboxylate transporter (<scp>TTT</scp>) family in <i>Rhodopseudomonas palustris</i>

et al. 2020

Preprint

Background The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analyzing 106 metagenomes from 30 sampling points distributed along the river.Results We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.Conclusions Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers.

Section: Discussionsupporting

confidence: 47%

Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter

et al. 2020

Preprint

“…In particular, previous studies showed that the TTT system was present in high quantities in the Amazon River, and this was attributed to a potential degradation of allochthonous organic matter [38]. Recent findings also suggest a TTT system related to the transport of TeOM degradation byproducts [39,40]. Little is known about these transporters, but our findings indicate that TTT is an abundant protein family in the Amazon River, suggesting that tricarboxylates are a common carbon source for prokaryotes in these waters.…”

Section: Discussionsupporting

confidence: 47%

“…Similarly to the fate of hemi-/cellulose degradation byproducts, lignin degradation ends up in the production of 4-carboxy-4hydroxy-2-oxoadipate, which is converted into pyruvate or oxaloacetate, both substrates of the tricarboxylic acid cycle (TCA) [36]. Recently, several substrate binding proteins (TctC) belonging to the tripartite tricarboxylate transporter (TTT) system were associated to the transport of TeOM degradation byproducts, like adipate [39] and terephthalate [40]. To investigate the metabolism of these compounds, and the possible link between the TTT system and lignin/cellulose degradation, the protein families TctA (PF01970), TctB (PF07331) and TctC (PF03401)…”

Section: Teom Degradation Machinerymentioning

confidence: 99%

Uncovering the gene machinery of the Amazon River microbiome to degrade rainforest organic matter

et al. 2019

Preprint

Background: The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analyzing 106 metagenomes from 30 stations distributed along the river. Results: We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant sampled environments (rivers and rainforest soil). Analyses of TeOM-degradation genes revealed that lignin degradation pathways correlated to tricarboxylates and hemicellulose processing, pointing to a higher lignin degradation coupled to the consumption of labile compounds. We propose a model on how the degradation of recalcitrant TeOM modulated by labile compounds (i.e. priming effect) may operate in the Amazon River waters. Conclusions: Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its role in TeOM degradation. Furthermore, the AMnrGC represents an important resource for future works exploring the links between TeOM and its degradation by aquatic microbiotas in tropical ecosystems.

“…In particular, previous studies showed that the TTT system was present in high quantities in the Amazon River, and this was attributed to a potential degradation of allochthonous organic matter [14]. Recent ndings also suggest a TTT system related to the transport of TeOM degradation byproducts [46,47]. Little is known about these transporters, but our ndings indicate that TTT is an abundant protein family in the Amazon River, suggesting that tricarboxylates are a common carbon source for prokaryotes in these waters.…”

Section: Discussionmentioning

confidence: 46%

“…Similarly to the fate of hemi-/cellulose degradation byproducts, lignin degradation ends up in the production of 4-carboxy-4hydroxy-2-oxoadipate, which is converted into pyruvate or oxaloacetate, both substrates of the tricarboxylic acid cycle (TCA) [44]. Recently, several substrate binding proteins (TctC) belonging to the tripartite tricarboxylate transporter (TTT) system were associated with the transport of TeOM degradation byproducts, like adipate [46] and terephthalate [47]. To investigate the metabolism of these compounds, and the possible link between the TTT system and lignin/cellulose degradation, the protein families TctA (PF01970), TctB (PF07331) and TctC (PF03401) were searched in PFAM.…”

Section: Potential Teom Degradation Machinerymentioning

confidence: 99%

Uncovering the Genomic Potential of the Amazon River Microbiome to Degrade Rainforest Organic Matter

et al. 2020

Preprint

Background: The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analyzing 106 metagenomes from 30 sampling points distributed along the river.Results: We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.Conclusions: Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers.