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

2019 ◽  
Author(s):  
Célio Dias Santos ◽  
Hugo Sarmento ◽  
Fernando Pellon de Miranda ◽  
Flávio Henrique-Silva ◽  
Ramiro Logares
Keyword(s):  
Organic Matter ◽  
Lignin Degradation ◽  
Amazon River ◽  
Spatial Distributions ◽  
Gene Repertoire ◽  
Terrestrial Organic Matter ◽  
Incubation Experiments ◽  
Degradation Rates ◽  
Redundant Genes ◽  
Gene Functions

ABSTRACTThe Amazon River receives, from the surrounding rainforest, huge amounts of terrestrial organic matter (TeOM), which is typically resistant to microbial degradation. However, only a small fraction of the TeOM ends up in the ocean, indicating that most of it is degraded in the river. So far, the nature of the genes involved in TeOM degradation and their spatial distributions are barely known. Here, we examined the Amazon River microbiome gene repertoire and found that it contains a substantial gene-novelty, compared to other environments (rivers and rainforest soil). We predicted ~3.7 million non-redundant genes, affiliating mostly to bacteria. The gene-functions involved in TeOM degradation revealed that lignin degradation correlated to tricarboxylates and hemicellulose processing, pointing to higher lignin degradation rates under consumption of labile compounds. We describe the biochemical machinery that could be speeding up the decomposition of recalcitrant compounds in Amazonian waters, previously reported only in incubation experiments.

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

2019 ◽  
Author(s):  
Célio Dias Santos Júnior ◽  
Hugo Sarmento ◽  
Fernando Pellon de Miranda ◽  
Flávio Henrique-Silva ◽  
Ramiro Logares
Keyword(s):  
Organic Matter ◽  
Priming Effect ◽  
Lignin Degradation ◽  
Amazon River ◽  
Terrestrial Organic Matter ◽  
River Waters ◽  
Gene Catalogue ◽  
Redundant Genes ◽  
The World ◽  
Redundant Gene

Abstract 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.

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

2020 ◽  
Author(s):  
Célio Dias Santos Júnior ◽  
Hugo Sarmento ◽  
Fernando Pellon de Miranda ◽  
Flávio Henrique-Silva ◽  
Ramiro Logares
Keyword(s):  
Organic Matter ◽  
Future Research ◽  
Amazon River ◽  
Terrestrial Organic Matter ◽  
River Waters ◽  
Gene Catalogue ◽  
Redundant Genes ◽  
Hemicellulose Degradation ◽  
Genes Encoding ◽  
Redundant Gene

Abstract 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.

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

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Célio Dias Santos-Júnior ◽  
Hugo Sarmento ◽  
Fernando Pellon de Miranda ◽  
Flávio Henrique-Silva ◽  
Ramiro Logares
Keyword(s):  
Organic Matter ◽  
Future Research ◽  
Amazon River ◽  
Terrestrial Organic Matter ◽  
River Waters ◽  
Gene Catalogue ◽  
Redundant Genes ◽  
Hemicellulose Degradation ◽  
Genes Encoding ◽  
Redundant Gene

Abstract 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 analysing 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.

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

2020 ◽  
Author(s):  
Célio Dias Santos Júnior ◽  
Hugo Sarmento ◽  
Fernando Pellon de Miranda ◽  
Flávio Henrique-Silva ◽  
Ramiro Logares
Keyword(s):  
Organic Matter ◽  
Future Research ◽  
Amazon River ◽  
Terrestrial Organic Matter ◽  
River Waters ◽  
Gene Catalogue ◽  
Redundant Genes ◽  
Hemicellulose Degradation ◽  
Genes Encoding ◽  
Redundant Gene

Abstract 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.

scholarly journals Transport and fate of different components of terrestrial organic matter across the Siberian-Arctic shelves

2020 ◽  
Author(s):  
Örjan Gustafsson ◽  
Igor Semiletov ◽  
Natalia Shakhova ◽  
Oleg Dudarev ◽  
Jorien Vonk ◽  
...  
Keyword(s):  
Organic Matter ◽  
Landscape Heterogeneity ◽  
Oxidation Products ◽  
Terrestrial Organic Matter ◽  
Inverse Approach ◽  
Degradation Rates ◽  
Siberian Arctic ◽  
Global Soil ◽  
Shelf Sea ◽  
Dependent Transport

<p>About one-third to half of the global soil carbon is held in the top 1-3 m of tundra+taiga permafrost PF (~1000 Pg-C) with deeper layers below as Deep-PF (~400 Pg-C) and in Pleistocene Ice Complex Deposit permafrost (ICD-PF, ~400 Pg-C), lining 4000 km of the East Siberian Arctic coast.  In order to overcome the landscape heterogeneity and the stochastic nature of e.g. erosional release processes, we use the East Siberian Arctic Shelf (ESAS) in an inverse approach – as a natural integrator of the TerrOM releases from both the river drainage basins and from the erosion of ICD-containing bluffs. We are exploring how source-dependent transport and translocated degradation affect the released TerrOM.</p><p> </p><p>The sources of released terrOM have been increasingly constrained using great rivers and the ESAS as natural integrators through a combination of biomarkers and δ<sup>13</sup>C/Δ<sup>14</sup>C on bulk-C and on compound level. There are significant gradients in sources both E-W and S-N across each shelf sea and between water column DOM, POM and sedimentary OM. The largest source of OC to ESAS sediments is not rivers or marine plankton – it is coastal erosion of old ICD.  Our initial limited dataset has now been much expanded, as has the end-member database while the statistical source apportionment method has been refined. They combine to show more efficient cross-shelf transport of river-borne “topsoil-PF” compared to ICD-PF and a clear distinction in sources of TerrOM between western and eastern ESAS regimes separated roughly along 165E, consistent with the local oceanography.</p><p>There have been good strides also in understanding degradation of TerrOM exported to ESAS. Studies are demonstrating continuous offshoreward degradation of all TerrOM, yet with large differences between compound classes. Physical association of TerrOM with different sediment components, and sorting of the sediments exert first-order control on TerrOM distribution and degradation. An expanded dataset on specific surface area (SSA) and CuO oxidation products reveals spatial patterns across ESAS. The combination of compound-specific radiocarbon analysis of terrestrial biomarkers with SSA-normalized TerrOM signals constrains the ambient degradation rates and fluxes during the 3-4000 year timescale of cross-shelf transport. The degradation of TerrOM also causes severe ocean acidification of the ESAS.</p><p>Investigations of sources and fate of TerrOM on the ESAS – the World’s largest shelf sea– provides a window to constrain permafrost-C remobilization and to study mechanisms of transport and degradability of different components of released terrestrial organic matter.</p>

scholarly journals Linking microbial genomes with their potential to degrade terrestrial organic matter in the Amazon River

2020 ◽  
Author(s):  
Celio Dias Santos-Junior ◽  
Ramiro Logares ◽  
Flavio Henrique-Silva
Keyword(s):  
Organic Matter ◽  
Aquatic Ecosystems ◽  
Oxidation Process ◽  
Cellulose Degradation ◽  
Amazon River ◽  
Terrestrial Organic Matter ◽  
Microbial Genomes ◽  
Lignin Oxidation ◽  
Microbial Consumption ◽  
Structural Carbon

Abstract Rivers connect the carbon cycle in land with that in aquatic ecosystems by transporting and transforming terrestrial organic matter (TeOM). The Amazon River receives huge loads of TeOM from the surrounding rainforest, promoting a substantial microbial heterotrophic activity and consequently, CO2 outgassing. In the Amazon River, microbes degrade up to 55% of the lignin present in the TeOM. Yet, the main microbial genomes involved in TeOM degradation were not known. Here, we characterize 51 population genomes (PGs) representing some of the most abundant microbes in the Amazon River deriving from 106 metagenomes. The 51 reconstructed PGs are among the most abundant microbes in the Amazon River, and 53% of them are not able to degrade TeOM. Among the PGs capable of degrading TeOM, 20% were exclusively cellulolytic, while the others could also oxidize lignin. The transport and consumption of lignin oxidation byproducts seemed to be decoupled from the oxidation process, being apparently performed by different groups of microorganisms. Altogether, based on our findings, we suggest a new priming effect model that explains the quick turnover of TeOM as a product of the microbial consumption of lignin-derived aromatic compounds produced by lignin oxidation, reducing the inhibition of cellulose degradation and ensuring structural carbon and energy for cell growth. By connecting the genomic features of abundant microbes in the Amazon River with the degradation of recalcitrant TeOM, we contribute to increase our understanding of the rapid consumption of recalcitrant compounds in this ecosystem.

Degradation of terrestrial organic matter by aquatic microbial genomes in the Amazon River

2020 ◽  
Author(s):  
Celio Dias Santos-Junior ◽  
Ramiro Logares ◽  
Flavio Henrique-Silva
Keyword(s):  
Organic Matter ◽  
Aquatic Ecosystems ◽  
Priming Effect ◽  
Oxidation Process ◽  
Microbial Consortium ◽  
Amazon River ◽  
Terrestrial Organic Matter ◽  
Genomic Features ◽  
Microbial Genomes ◽  
By Products

Abstract Rivers connect the carbon cycle in land with that in aquatic ecosystems by transporting and transforming terrestrial organic matter (TeOM). The Amazon River receives huge loads of TeOM from the surrounding rainforest, promoting a substantial microbial heterotrophic activity and consequently, CO2 outgassing. In the Amazon River, microbes degrade up to 55% of the lignin present in the TeOM. Yet, the main microbial genomes involved in TeOM degradation were unknown. Here, we characterize 51 Population Genomes (PGs) representing some of the most abundant microbes in the Amazon River deriving from 106 metagenomes. The 51 reconstructed PGs are among the most abundant microbes in the Amazon River, and 53% of them are not able to degrade TeOM. Among the PGs capable of degrading TeOM, 20% were exclusively cellulolytic, while the others could also oxidize lignin. The transport and consumption of lignin oxidation by-products seemed to be decoupled from the oxidation process, being apparently performed by different groups of microorganisms. By connecting the genomic features of abundant microbes in the Amazon River with the degradation machinery of TeOM, we suggest that a microbial consortium following a priming effect model could explain the quick turnover of TeOM previously observed in this ecosystem.

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