Aerobic Hydrocarbon-Degrading Gammaproteobacteria: Xanthomonadales

Gutiérrez, Tony

doi:10.1007/978-3-030-14796-9_4

Cited by 12 publications

(6 citation statements)

References 52 publications

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“…The initial phase of bloom development of Microcystis coincided with an increase in microbial cluster numbers and included members of the ammoniaoxidizing Nitrosomonadales order (Cluster 1, Methyloversatilis discipulorum). Moreover, the decrease in the absolute abundance of M. smithii and M. aeruginosa morphospecies during the end of the first stratification period coincided with an increase in the members of the hydrocarbondegrading gamma-proteobacteria Xanthomonadales (Cluster 4; Stenotrophomonas rhizophilia), which is similar to the observation by Gutierrez and co-authors 61 of the structure of Microcystis bloom-associated microbiomes.…”

Section: Microcystis-associated Microbiomessupporting

confidence: 85%

Dynamics of associated microbiomes during algal bloom development: to see and to be seeing

Meirkhanova,

Zhumakhanova,

Len

et al. 2023

Preprint

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Our understanding of the interactions between bacteria and phytoplankton in the freshwater phycosphere, including the development of algal blooms, is very limited. To identify the taxa and compositional variation within microbial communities, we performed 16S rRNA amplicon sequencing research on samples collected weekly through summer from mesocosms that differed in temperature and mixing regimes. We investigated, for the first time, the abundance diversity of microalgae, including Chlorophyta, Cryptophyta, and Cyanobacteria species, using visualization-based FlowCAM analysis and classification of microbial communities to species level by nanopore next-generation sequencing. We found that nanopore metagenomics, in parallel with complementary imaging flow cytometry, can depict the fine temporal dynamics of microbiomes associated with visually identified Microcystis morphospecies, Chlorophyta, and Cryptophyta during algal bloom development. Our results showed that the temporal characteristics of microbiomes combined with a visual approach may be a key tool to predict the metacommunity structure and dynamics of algal blooms in response to anthropogenic effects and climate change.

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Section: Microcystis-associated Microbiomessupporting

confidence: 85%

Dynamics of associated microbiomes during algal bloom development: to see and to be seeing

Meirkhanova,

Zhumakhanova,

Len

et al. 2023

Preprint

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“…Finally, putative degraders of artificially aged OXO (AA 144 OXO) belonged to Gammaproteobacteria, Cellvibrionaceae, Myxococcales, and Flavobacteriaceae, which are classically observed on the plastisphere of various material types found in seawaters including PE ( Zettler et al, 2013 ), PET ( Oberbeckmann et al, 2016 ), and PVC ( Pinto et al, 2019 ). Members of Myxococcales and Flavobacteriaceae presented high hydrolytic enzymes excretion and complex biopolymers degradation capacities ( Shimkets et al, 2006 ; Amaral-Zettler et al, 2020 ) together with hydrocarbon degradation capabilities ( Pollet et al, 2018 ; Gutierrez, 2019 ). We are aware that the description of putative OTUs involved in the biodegradation of PCL, PHBV, and AA-OXO are sometimes limited to the poor taxonomic identification based on 16S rRNA metabarcoding; however, it opens new routes for further studies to delve deeper into the understanding of the biodegradability of these materials in seawaters.…”

Section: Discussionmentioning

confidence: 99%

Bacterial Abundance, Diversity and Activity During Long-Term Colonization of Non-biodegradable and Biodegradable Plastics in Seawater

et al. 2021

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The microorganisms living on plastics called “plastisphere” have been classically described as very abundant, highly diverse, and very specific when compared to the surrounding environments, but their potential ability to biodegrade various plastic types in natural conditions have been poorly investigated. Here, we follow the successive phases of biofilm development and maturation after long-term immersion in seawater (7 months) on conventional [fossil-based polyethylene (PE) and polystyrene (PS)] and biodegradable plastics [biobased polylactic acid (PLA) and polyhydroxybutyrate-co-hydroxyvalerate (PHBV), or fossil-based polycaprolactone (PCL)], as well as on artificially aged or non-aged PE without or with prooxidant additives [oxobiodegradable (OXO)]. First, we confirmed that the classical primo-colonization and growth phases of the biofilms that occurred during the first 10 days of immersion in seawater were more or less independent of the plastic type. After only 1 month, we found congruent signs of biodegradation for some bio-based and also fossil-based materials. A continuous growth of the biofilm during the 7 months of observation (measured by epifluorescence microscopy and flow cytometry) was found on PHBV, PCL, and artificially aged OXO, together with a continuous increase in intracellular (3H-leucine incorporation) and extracellular activities (lipase, aminopeptidase, and β-glucosidase) as well as subsequent changes in biofilm diversity that became specific to each polymer type (16S rRNA metabarcoding). No sign of biodegradation was visible for PE, PS, and PLA under our experimental conditions. We also provide a list of operational taxonomic units (OTUs) potentially involved in the biodegradation of these polymers under natural seawater conditions, such as Pseudohongiella sp. and Marinobacter sp. on PCL, Marinicella litoralis and Celeribacter sp. on PHBV, or Myxococcales on artificially aged OXO. This study opens new routes for a deeper understanding of the polymers’ biodegradability in seawaters, especially when considering an alternative to conventional fossil-based plastics.

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“…However, the alkane-degrading taxa identified in Liu et al (2019) were not detected in sediment rDNA or rRNA libraries of this study. Instead, we identified several OTUs in sediments of the Mariana Trench, belonging to Planomicrobium , Xanthomonadales, Anaerolineaceae, and SAR202 clade ( Figure 6 and Supplementary Table S5 ), members of which have been reported to be active or as potential alkane-degraders in aerobic or anaerobic conditions ( Engelhardt et al, 2001 ; Head et al, 2006 ; Liang et al, 2015 ; Gutierrez, 2017 ; Landry et al, 2017 ). OTUs from Planomicrobium , Anaerolineaceae, and SAR202 were among the top 20 most dominant members in the rRNA libraries of MT samples ( Figure 6 ), and members of Anaerolineaceae and Xanthomonadales were identified as keystone taxa in the co-occurrence network of potentially active prokaryotic community ( Figure 7A and Supplementary Table S5 ), suggesting the important role of these hydrocarbon-degrading bacteria in supporting the function and structure of active prokaryotic communities in the sediment of MT.…”

Section: Discussionmentioning

confidence: 99%

Bulk and Active Sediment Prokaryotic Communities in the Mariana and Mussau Trenches

Liu

Wang

et al. 2020

Front. Microbiol.

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Surprisingly high rates of microbial respiration have recently been reported in hadal trench sediment, yet the potentially active microorganisms and specific microbe–microbe relationships in trench sediment are largely unknown. We investigated the bulk and active prokaryotic communities and co-occurrence interactions of different lineages in vertically sectioned sediment cores taken from the deepest points of the Mariana and Mussau Trenches. Analysis on species novelty revealed for the first time the high rate of novel lineages in the microbial communities of the hadal trenches. Using 95, 97, and 99% similarity as thresholds, averagely 22.29, 32.3, and 64.1% of total OTUs retrieved from sediments of the two trenches were identified as the potentially novel lineages, respectively. The compositions of the potentially active communities, revealed via ribosomal RNA (rRNA), were significantly different from those of bulk communities (rDNA) in all samples from both trenches. The dominant taxa in bulk communities generally accounted for low proportions in the rRNA libraries, signifying that the abundance was not necessarily related to community functions in the hadal sediments. The potentially active communities showed high diversity and composed primarily of heterotrophic lineages, supporting their potential contributions in organic carbon consumption. Network analysis revealed high modularity and non-random co-occurrence of phylogenetically unrelated taxa, indicating highly specified micro-niches and close microbial interactions in the hadal sediments tested. Combined analysis of activity potentials and network keystone scores revealed significance of phyla Chloroflexi and Gemmatimonadetes, as well as several potentially alkane-degrading taxa in maintaining microbial interactions and functions of the trench communities. Overall, our results demonstrate that the hadal trenches harbor diverse, closely interacting, and active microorganisms, despite the extreme environmental conditions.

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Aerobic Hydrocarbon-Degrading Gammaproteobacteria: Xanthomonadales

Cited by 12 publications

References 52 publications

Dynamics of associated microbiomes during algal bloom development: to see and to be seeing

Dynamics of associated microbiomes during algal bloom development: to see and to be seeing

Bacterial Abundance, Diversity and Activity During Long-Term Colonization of Non-biodegradable and Biodegradable Plastics in Seawater

Bulk and Active Sediment Prokaryotic Communities in the Mariana and Mussau Trenches

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