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 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 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 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 A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses

2018 ◽  
Author(s):  
Felix Hausera ◽  
Paulo H. O. Ceciliatoa ◽  
Yi-Chen Lin ◽  
DanDan Guo ◽  
JD Gregerson ◽  
...  
Keyword(s):  
Genetic Screens ◽  
Resource Center ◽  
New Genes ◽  
Redundant Genes ◽  
Forward Genetic Screens ◽  
Genes Encoding ◽  
Arabidopsis Biological Resource Center ◽  
Redundant Gene ◽  
Aba Insensitive ◽  
Arabidopsis Biological Resource

AbstractThe identification of homologous genes with functional overlap in forward genetic screens is severely limited. Here we report the generation of over 14,000 amiRNA-expressing plants that enable screens of the functionally redundant gene space in Arabidopsis. A protocol is developed here for isolating robust and reproducible amiRNA-mutants. Examples of validation approaches and essential controls are presented for two new amiRNA mutants that exhibit genetically redundant phenotypes and circumvent double mutant lethality. In a forward genetic screen for abscisic acid (ABA)-mediated inhibition of seed germination, amiRNAs that target combinations of known redundant ABA receptor and SnRK2 kinase genes were rapidly isolated, providing a strong proof of principle for this approach. A new ABA insensitive amiRNA line is isolated, which targets three genes encoding avirulence-induced gene2-like (AIG2) genes. A thermal imaging screen for plants with impaired stomatal opening in response to low CO2 exposure led here to isolation of a new amiRNA targeting two essential proteasomal subunits, PAB1 and PAB2. The seed library of 14,000 T2 amiRNA lines generated here provides a new platform for forward genetic screens and is being made available to the Arabidopsis Biological Resource Center (ABRC) and optimized procedures for amiRNA screening and controls are described.HighlightThe generation of over 14,000 amiRNA-expressing plants is reported that are being made publicly available enabling screens of redundant genes in Arabidopsis. Identification of known and new genes is reported.

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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