Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems

Yuan, Heyang; Mei, Renwei; Liao, Junhui; Liu, Wen Tso

doi:10.3389/fmicb.2019.01536

Cited by 46 publications

(28 citation statements)

References 50 publications

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“…Thus, we can conclude that the shift from a disturbed to an undisturbed ecosystem increased the contribution of drift. Our observations corroborate other investigations of bioreactors (15,50) and simulations (51) that report that stochasticity is fundamental for the assembly of communities. However, the finding that drift was important for structuring the undisturbed microcosms was unexpected.…”

Section: Discussionsupporting

confidence: 91%

The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities

Gundersen

Morelan

Andersen

et al. 2021

Preprint

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Understanding how periodical disturbances affect the community assembly processes is vital for predicting temporal dynamics in microbial communities. The effect of dilutions as disturbances are poorly understood. We used a marine bacterial community to investigate the effect of disturbance (+/-) and carrying capacity (high/low) over 50 days in a dispersal-limited 2x2 factorial crossover study in triplicates. The community's disturbance regime was crossed halfway. We modelled the rate of change in community composition between replicates and used this rate to quantify selection and ecological drift. The disturbed communities increased in Bray-Curtis similarity with 0.011+/-0.0045 (Period 1) and 0.0092+/-0.0080 day-1 (Period 2), indicating that selection dominated community assembly. The undisturbed communities decreased in similarity at a rate of -0.015+/-0.0038 day-1 in Period 1 and were stable in Period 2 at 0.00050+/-0.0040 day-1, suggesting drift structured community assembly. Interestingly, carrying capacity had minor effects on community dynamics. This study is the first to show that stochastic effects are suppressed by periodical disturbances resulting in exponential growth periods due to density-independent biomass loss and resource input. The increased contribution of selection as a response to disturbances implies that ecosystem prediction is achievable.

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Section: Discussionsupporting

confidence: 91%

The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities

Gundersen

Morelan

Andersen

et al. 2021

Preprint

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“…The EtOH-fed communities, on the other hand, were separated from the fructose/PEGfed communities since Batch 1 and remained stable throughout the enrichment. The signi cant difference in microbial communities agreed well with the system performance (Figure 1), highlighting the key role of the substrate as a deterministic factor that drives microbial community dynamics [34,65].…”

Section: Effects Of Enrichment On Microbial Population and Overall Acsupporting

confidence: 68%

“…Triplicate GAC samples were collected at the end of each batch and stored immediately at -80 °C before nucleic acid extraction. DNA extraction, library preparation, amplicon sequencing, and microbial community analyses were performed as previously described [33,34]. RNA was extracted following the manufacture's instruction (Qiagen) and puri ed with both RNase-free DNase Set (Qiagen) and Turbo DNAfree (Ambion).…”

Section: Nucleic Acid Extraction and Sequencingmentioning

confidence: 99%

Disentangling Syntrophic Electron Transfer Mechanisms in Methanogenesis Through Electrochemical Stimulation, Omics, and Machine Learning

Yuan¹,

Wang²,

Lin³

et al. 2021

Preprint

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Background: Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. Results: To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, acetate accumulated in all reactors, while propionate was detected only in the electrochemical reactors. Four dominant fermentative bacteria were identified in the core population, and metatranscriptomics analysis suggested that they were responsible for the degradation of fructose and ethanol to propionate, propanol, acetate, and H2. Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation. The results thus confirmed Ca. G. eutrophica’s EET ability. The high-quality draft genome (completeness 99.4%, contamination 0.6%) further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. Redundancy analysis and a Bayesian network constructed with the core population predicted the importance of Ca. G. eutrophica-related OTU650 to methane production. The Bayesian network modeling approach was also applied to the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis.Conclusions: Ca. G. eutrophica is electroactive and simultaneously performs IHT and DIET. The results from the metatranscriptomic analysis have provided valuable information for enrichment and isolation of Ca. G. eutrophica. IHT is predicted to have a stronger impact on methane production than DIET in the electrochemical reactors. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.

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“…The occurrence of stochastic events could be relevant in systems with high dispersal under strongly selecting conditions ( 43 ), such as lignocellulose-enriched liquid cultures. Nevertheless, to confirm this statement, it would be necessary to carry out well-replicated experiments and null deviation analysis in order to obtain robust conclusions ( 44 , 45 ).…”

Section: Discussionmentioning

confidence: 99%

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium

Díaz-García

Huang

Spröer

et al. 2021

Appl Environ Microbiol

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The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid media with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After a subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (> 99%) within the MELMC, indicating that these are the key players of degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secrete an array of endo-enzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition next to an analysis of carbohydrate-active enzymes of twenty bacterial genomes supports the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp. IMPORTANCE The significance of our study mainly lies on the development of a combined top-down enrichment strategy (i.e. dilution-to-stimulation coupled to dilution-to-extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive an effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e. release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.

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Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems

Cited by 46 publications

References 50 publications

The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities

The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities

Disentangling Syntrophic Electron Transfer Mechanisms in Methanogenesis Through Electrochemical Stimulation, Omics, and Machine Learning

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium

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