Enrichment of Aquatic Xylan-Degrading Microbial Communities
Abstract
:1. Introduction
2. Material and Methods
2.1. Sampling and Site Description
2.2. Substrate Preparation
2.3. Bacterial Enrichment
2.4. Metagenomic Sequencing
2.5. Gel Permeation Chromatography
3. Results and Discussion
3.1. Polysaccharide Degradation and Bacterial Growth
3.2. Taxonomic Profiling
3.3. Enrichment of Genes Associated with Xylan Degradation and Catabolism
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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OS | WAX1 | WAX4 | BEX1 | BEX4 | |
---|---|---|---|---|---|
Total reads | 10,924,419 | 18,135,162 | 14,350,049 | 16,357,164 | 19,858,928 |
Classified reads (%) | 45.32% | 61.96% | 49.70% | 72.67% | 27.26% |
of which: | |||||
- Classified kingdom (%) | 98.33% | 99.20% | 98.91% | 99.17% | 95.81% |
- Classified species (%) | 40.86% | 50.56% | 50.49% | 38.17% | 51.38% |
Classified species (reads) | 2,022,805 | 5,680,604 | 3,600,769 | 4,536,935 | 2,781,849 |
Shannon Diversity Index (H) | 4.73 | 4.76 | 5.23 | 4.00 | 4.91 |
Shannon Equitability Index (E) | 0.51 | 0.52 | 0.58 | 0.44 | 0.56 |
Species (all) | 9095 | 8592 | 7258 | 8557 | 6241 |
>100 reads | 2175 | 2565 | 2883 | 1259 | 2057 |
>5000 reads | 51 | 105 | 85 | 66 | 41 |
>20,000 reads | 12 | 33 | 16 | 27 | 20 |
Phylum | Class | Species | % OS | % WAX1 | % WAX4 | % BEX1 | % BEX4 |
---|---|---|---|---|---|---|---|
Actinomycetota | Actinomycetes | Mycobacterium canettii | 0.74 | 0.31 | 0.41 | 0.22 | 2.27 |
Bacillota | Bacilli | Exiguobacterium mexicanum | 0.00 | 1.64 | 0.00 | 0.00 | 0.00 |
Bacillota | Bacilli | Leuconostoc mesenteroides | 0.00 | 1.17 | 0.00 | 0.00 | 0.00 |
Bacillota | Bacilli | Niallia circulans | 0.00 | 4.94 | 8.55 | 0.02 | 0.04 |
Bacillota | Clostridia | Clostridium intestinale | 0.00 | 0.51 | 0.00 | 1.14 | 0.00 |
Bacteroidota | Flavobacteriia | Cloacibacterium caeni | 0.00 | 2.75 | 0.00 | 0.32 | 0.00 |
Bacteroidota | Flavobacteriia | Cloacibacterium normanense | 0.00 | 1.20 | 0.00 | 0.15 | 0.00 |
Bacteroidota | Sphingobacteriia | Sphingobacterium hotanense | 0.00 | 2.10 | 0.00 | 0.24 | 0.00 |
Campylobacterota | Epsilonproteobacteria | Arcobacter suis | 1.14 | 0.00 | 0.00 | 0.00 | 0.00 |
Campylobacterota | Epsilonproteobacteria | Arcobacter venerupis | 1.82 | 0.00 | 0.00 | 0.00 | 0.00 |
Pseudomonadota | Alphaproteobacteria | Acetobacter aceti | 0.00 | 0.00 | 0.01 | 0.00 | 2.42 |
Pseudomonadota | Alphaproteobacteria | Acetobacter ghanensis | 0.00 | 0.00 | 0.00 | 0.00 | 3.91 |
Pseudomonadota | Alphaproteobacteria | Acetobacter orientalis | 0.00 | 0.00 | 0.00 | 0.00 | 1.45 |
Pseudomonadota | Alphaproteobacteria | Acetobacter persici | 0.00 | 0.00 | 0.00 | 0.00 | 2.26 |
Pseudomonadota | Alphaproteobacteria | Acetobacter vaccinii | 0.00 | 0.00 | 0.00 | 0.00 | 5.61 |
Pseudomonadota | Alphaproteobacteria | Gluconacetobacter diazotrophicus | 0.00 | 0.00 | 0.01 | 0.00 | 1.80 |
Pseudomonadota | Alphaproteobacteria | Komagataeibacter saccharivorans | 0.00 | 0.00 | 0.00 | 0.00 | 1.16 |
Pseudomonadota | Alphaproteobacteria | Komagataeibacter xylinus | 0.00 | 0.00 | 0.00 | 0.00 | 1.67 |
Pseudomonadota | Alphaproteobacteria | Rhodobacter capsulatus | 0.01 | 0.01 | 2.45 | 0.00 | 0.03 |
Pseudomonadota | Alphaproteobacteria | Rhodobacter sp. LPB0142 | 0.00 | 0.01 | 3.04 | 0.00 | 0.01 |
Pseudomonadota | Gammaproteobacteria | Acinetobacter calcoaceticus | 0.01 | 0.01 | 1.66 | 0.03 | 0.00 |
Pseudomonadota | Gammaproteobacteria | Acinetobacter indicus | 0.05 | 5.26 | 0.00 | 2.43 | 0.01 |
Pseudomonadota | Gammaproteobacteria | Acinetobacter radioresistens | 0.02 | 1.51 | 0.00 | 0.08 | 0.00 |
Pseudomonadota | Gammaproteobacteria | Acinetobacter sp. CS-2 | 0.20 | 1.10 | 0.00 | 7.19 | 0.11 |
Pseudomonadota | Gammaproteobacteria | Acinetobacter tibetensis | 0.01 | 0.01 | 0.00 | 3.43 | 0.06 |
Pseudomonadota | Gammaproteobacteria | Dickeya oryzae | 0.00 | 0.00 | 0.00 | 1.23 | 0.00 |
Pseudomonadota | Gammaproteobacteria | Dickeya zeae | 0.00 | 0.00 | 0.00 | 2.09 | 0.00 |
Pseudomonadota | Gammaproteobacteria | Pseudomonas fluorescens | 1.78 | 0.08 | 0.02 | 0.04 | 0.06 |
Pseudomonadota | Gammaproteobacteria | Stenotrophomonas maltophilia | 0.02 | 0.03 | 2.76 | 0.31 | 0.02 |
Pseudomonadota | Gammaproteobacteria | Tolumonas auensis | 0.00 | 0.02 | 0.00 | 2.43 | 0.00 |
Enzyme Name | Gene Orthology | KEGG Enzyme | Alpha-Proteob. | Beta-Proteob. | Gamma-Proteob. | Bacillota | Bacter-Oidota | Actino-Mycetota | Campylo-Bacterota |
---|---|---|---|---|---|---|---|---|---|
endo-1,4-beta-xylanase | GO:0031176 | K01181 | 24.4% | 4.4% | 19.5% | 35.5% | 66.5% | 85.0% | 0.0% |
xylan 1,4-beta-xylosidase | GO:0009044 | K01198 | 35.4% | 11.0% | 21.6% | 48.7% | 95.4% | 40.4% | 0.0% |
glucosylceramidase | GO:0004348 | K01201 | 1.5% | 2.8% | 6.0% | 16.0% | 91.2% | 21.5% | 0.0% |
alpha-L-arabinofuranosidase | GO:0046556 | K01209 | 25.4% | 6.3% | 7.4% | 45.0% | 60.6% | 46.0% | 0.0% |
arabinoxylan arabinofuranohydrolase | GO:0046556 | K15921 | 1.1% | 0.0% | 0.2% | 11.4% | 24.3% | 6.7% | 0.0% |
non-reducing end alpha-L-arabinofuranosidase | GO:0046556 | K20844 | 0.4% | 1.3% | 0.0% | 0.0% | 0.0% | 14.6% | 0.0% |
arabinan endo-1,5-alpha-L-arabinosidase | GO:0046558 | K06113 | 5.2% | 9.4% | 7.9% | 26.0% | 51.1% | 26.0% | 0.0% |
glucuronoarabinoxylan endo-1,4-beta-xylanase | GO:0033940 | K15924 | 0.0% | 0.3% | 2.3% | 8.1% | 7.5% | 4.5% | 0.0% |
alpha-glucuronidase | GO:0046559 | K01235 | 5.7% | 2.8% | 6.6% | 11.0% | 30.7% | 7.9% | 0.0% |
Class | Description | Reads (OS) | Reads (WAX4-OS) | Reads (WAX4-WAX1) |
---|---|---|---|---|
Carbohydrate metabolism | ||||
GO:0031222 | arabinan catabolic process | 259 | 5779 | 4595 |
GO:0046373 | L-arabinose metabolic process | 266 | 5181 | 4231 |
GO:0045493 | xylan catabolic process | 953 | 7667 | 5584 |
GO:0019568 | arabinose catabolic process | 292 | 2348 | 2259 |
GO:0030245 | cellulose catabolic process | 1163 | 6683 | 5314 |
GO:0042732 | D-xylose metabolic process | 1112 | 4424 | 4040 |
GO:0016052 | carbohydrate catabolic process | 1899 | 4631 | 1643 |
GO:0005975 | carbohydrate metabolic process | 41,423 | 14,756 | 9037 |
Carbohydrate saccharification | ||||
GO:0046556 | alpha-L-arabinofuranosidase activity | 577 | 8364 | 6624 |
GO:0031176 | endo-1,4-beta-xylanase activity | 291 | 3241 | 2487 |
GO:0004565 | beta-galactosidase activity | 1074 | 5758 | 4123 |
GO:0009044 | xylan 1,4-beta-xylosidase activity | 372 | 2764 | 1895 |
GO:0008422 | beta-glucosidase activity | 1877 | 5069 | 941 |
GO:0030246 | carbohydrate binding | 7014 | 12,723 | 9705 |
GO:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | 5554 | 4159 | 1383 |
GO:0016787 | hydrolase activity | 36,954 | 23,813 | 15,266 |
Carbohydrate transport | ||||
GO:0015611 | ABC-type D-ribose transporter activity | 2616 | 12,337 | 12,575 |
GO:0015612 | ABC-type L-arabinose transporter activity | 928 | 2416 | 2652 |
GO:0042626 | ATPase-coupled transmembrane transporter activity | 6621 | 13,762 | 6725 |
GO:0055085 | transmembrane transport | 43,304 | 80,099 | 56,900 |
GO:0140359 | ABC-type transporter activity | 17,367 | 23,676 | 17,570 |
GO:0055052 | ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing | 43,637 | 52,747 | 56,871 |
GO:0043190 | ATP-binding cassette (ABC) transporter complex | 30,202 | 26,827 | 31,571 |
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Gaenssle, A.L.O.; Bertran-Llorens, S.; Deuss, P.J.; Jurak, E. Enrichment of Aquatic Xylan-Degrading Microbial Communities. Microorganisms 2024, 12, 1715. https://doi.org/10.3390/microorganisms12081715
Gaenssle ALO, Bertran-Llorens S, Deuss PJ, Jurak E. Enrichment of Aquatic Xylan-Degrading Microbial Communities. Microorganisms. 2024; 12(8):1715. https://doi.org/10.3390/microorganisms12081715
Chicago/Turabian StyleGaenssle, Aline Lucie Odette, Salvador Bertran-Llorens, Peter Joseph Deuss, and Edita Jurak. 2024. "Enrichment of Aquatic Xylan-Degrading Microbial Communities" Microorganisms 12, no. 8: 1715. https://doi.org/10.3390/microorganisms12081715