Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions

Effects of simulated warming on soil microbial community diversity and composition across diverse ecosystems

Soil warming can directly affect the microbial community, or indirectly affect the microbial community by affecting soil moisture, nutrient availability, vegetation growth, etc. However, the response of microorganisms to soil warming is complex, and there is no uniform conclusion on the impact and mechanism of warming on microbial diversity. As the global climate gradually warms, a comprehensive assessment of warming on soil microbial community changes is essential to understand and predict the response of microbial geochemical processes to soil warming. Here, we perform a meta-analysis of studies to investigate changes in soil microbial communities along soil warming gradients and the response of soil microbes to elevated temperature in different ecosystems. We found that the α diversity index of soil microorganisms decreased significantly with the increase in temperature, and the β diversity altered with the increase in soil temperature and the shifts in ecosystem. Most bacteria only alter when the temperature rises higher. Compared to the non-warming condition, the relative abundance of Acidobacteria, Proteobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia decreased by 19 %, 11 %, 19 %, 8 % and 6 %, respectively, and the relative abundance of Firmicutes increased by 34 %. Compared to farmland, forest, grassland and tundra ecosystems, soil microorganisms in wetland ecosystems were more sensitive to temperature increase, and the changes in bacteria were consistent with the overall alterations. This meta-analysis revealed significant changes in the composition of microbial communities on soil warming. With the decrease in biodiversity under increasing temperature conditions, these dominant microbiomes, which can grow well under high-temperature conditions, will play a stronger role in regulating nutrient and energy flow. Our analysis adds a global perspective to the temperature response of soil microbes, which is critical to improving our understanding of the mechanisms of how soil microbes change in response to climate warming.

A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester

Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.

Biochemical methane potential and active microbial communities during anaerobic digestion of biodegradable plastics at different inoculum-substrate ratios

The influence of the inoculum-substrate ratio (ISR) on the mesophilic and thermophilic biochemical methane potential test of two biodegradable plastics was evaluated. Poly(lactic acid) (PLA) and polyhydroxybutyrate (PHB) were selected for this study, the first for being recalcitrant to mesophilic anaerobic digestion (AD) and the second, by contrast, for being readily biodegradable. Several ISRs, calculated on the basis of volatile solids (VS), were tested: 1, 2, 2.85, 4, and 10 g(VS of inoculum).g(VS of substrate)^-1. A high ISR was associated with an enhanced methane production rate (i.e., biodegradation kinetics). However, the ultimate methane production did not change, except when inhibition was observed. Indeed, applying the lowest ISR to readily biodegradable plastics such as PHB resulted in inhibition of methane production. Based on these experiments, in order to have reproducible degradation kinetics and optimal methane production, an ISR between 2.85 and 4 is recommended for biodegradable plastics. The active microbial communities were analyzed, and the active bacteria differed depending on the plastic digested (PLA versus PHB) and the temperature of the process (mesophilic versus thermophilic). Previously identified PHB degraders (Ilyobacter delafieldii and Enterobacter) were detected in PHB-fed reactors. Thermogutta and Tepidanaerobacter were detected during the thermophilic AD of PLA, and they are probably involved in PLA hydrolysis and lactate conversion, respectively.

pH Regulates the Formation and Hatching of Cryptocaryon irritans Tomonts, Which Affects Cryptocaryoniasis Occurrence in Larimichthys crocea Aquaculture

Cryptocaryon irritans are the main pathogens of white spot disease in marine teleost. However, the occurrence of cryptocaryoniasis is influenced by several abiotic factors including the pH. To explore the effect of pH on the life cycle of C. irritans (encystment, cleavage, and hatchability), protomonts and tomonts of C. irritans were incubated in seawater of 10 different pH levels (2-11). pH 8 was used as the control. The change in morphology and infectivity of theronts that hatched from tomonts against Larimichthys crocea were then recorded. We found that pH 6-9 had no significant effect on the encystment, cleavage, and hatching of the parasites. However, pH beyond this limit decreased the cleavage and hatching of the tomonts. Furthermore, extreme pH decreased the number of theronts hatched by each tomont and the pathogenicity of the theronts, but increased the aspect ratio of the theronts. Infectivity experiments further revealed that extreme pH significantly decreased the infectivity of C. irritans against L. crocea. In conclusion, the C. irritans can survive in pH of 5 to 10, but pH 6-9 is the optimal range for the reproduction and infectivity of C. irritans. However, extreme pH negatively affects these aspects. IMPORTANCECryptocaryon irritans is a ciliate parasite that causes "white spot disease" in marine teleosts. The disease outbreak is influenced by hosts and a range of abiotic factors, such as temperature, salinity, and pH. Studies have shown that change in pH of seawater affects the structure (diversity and abundance of marine organisms) of marine ecosystem. However, how pH affects the life cycle and survival of C. irritans, and how future ocean acidification will affect the occurrence of cryptocaryoniasis, are not well understood. In this study, we explored the effect of pH on the formation and hatching of C. irritans tomonts. The findings of this study provide the foundation of the environmental adaptation of C. irritans, the occurrence of cryptocaryoniasis, and better management of marine fish culture.

Can anaerobic digestion be a suitable end-of-life scenario for biodegradable plastics? A critical review of the current situation, hurdles, and challenges

Growing concern regarding non-biodegradable plastics and the impact of these materials on the environment has promoted interest in biodegradable plastics. The intensification of separate biowastes collection in most European countries has also contributed to the development of biodegradable plastics, and the subject of their end-of-life is becoming a key issue. To date, there has been relatively little research to evaluate the biodegradability of biodegradable plastics by anaerobic digestion (AD) compared to industrial and home composting. However, anaerobic digestion is a particularly promising strategy for treating biodegradable organic wastes in the context of circular waste management. This critical review aims to provide an in-depth update of anaerobic digestion of biodegradable plastics by providing a summary of the literature regarding process performances, parameters affecting biodegradability, the microorganisms involved, and some of the strategies (e.g., pretreatment, additives, and inoculum acclimation) used to enhance the degradation rate of biodegradable plastics. In addition, a critical section is dedicated to suggestions and recommendations for the development of biodegradable plastics sector and their treatment in anaerobic digestion.

Methane production and active microbial communities during anaerobic digestion of three commercial biodegradable coffee capsules under mesophilic and thermophilic conditions

Biodegradable plastics market is increasing these last decades, including for coffee capsules. Anaerobic digestion, as a potential end-of-life scenario for plastic waste, has to be investigated. For this purpose, mesophilic (38 °C) and thermophilic (58 °C) anaerobic digestion tests on three coffee capsules made up with biodegradable plastic (Beanarella®, Launay® or Tintoretto®) and spent coffee (control) were compared by their methane production and the microbial communities active during the process. Mesophilic biodegradation of the capsules was slow and did not reach completion after 100 days, methane production ranged between 67 and 127 NL (CH₄) kg^-1 (VS). Thermophilic anaerobic digestion resulted in a better biodegradation and reached completion around 100 days, methane productions were between 257 and 294 NL (CH₄) kg^-1 (VS). The microbial populations from the reactors fed with plastics versus spent coffee grounds were significantly different, under both the mesophilic and the thermophilic conditions. However, the different biodegradable plastics only had a small impact on the main microbial community composition at a similar operational temperature and sampling time. Interestingly, the genus Tepidimicrobium was identified as a potential key microorganisms involved in the thermophilic conversion of biodegradable plastic in methane.

Sustained effect of zero-valent iron nanoparticles under semi-continuous anaerobic digestion of sewage sludge: Evolution of nanoparticles and microbial community dynamics

The effects of adding zero-valent iron nanoparticles (nZVI) on the physicochemical, biological and biochemical responses of a semi-continuous anaerobic digestion of sewage sludge have been assessed. Two sets of consecutive experiments of 103 and 116 days, respectively, were carried out in triplicate. nZVI were magnetically retained in the reactors, and the effect of punctual doses (from 0.27 to 4.33 g L^-1) over time was studied. Among the different parameters monitored, only methane content in the biogas was significantly higher when nZVI was added. However, this effect was progressively lost after the addition, and in 5-7 days, the methane content returned to initial values. The increase in the oxidation state of nanoparticles seems to be related to the loss of effect over time. Higher dose (4.33 g L^-1) sustained positive effects for a longer time along with higher methane content, but this fact seems to be related to microbiome acclimation. Changes in microbial community structure could also play a role in the mechanisms involved in methane enhancement. In this sense, the microbial consortium analysis reported a shift in the balance among acetogenic eubacterial communities, and a marked increase in the relative abundance of members assigned to Methanothrix genus, recognized as acetoclastic species showing high affinity for acetate, which explain the rise in methane content in the biogas. This research demonstrates that biogas methane enrichment in semicontinuous anaerobic digesters can be achieved by using nZVI nanoparticles, thus increasing energy production or reducing costs of a later biogas upgrading process.

New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus 'Methanomassiliicoccus armoricus MXMAG1'. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades ('free-living'/non-host-associated environmental clade and 'host-associated'/digestive clade) allowed us to explore the putative physiological traits of Candidatus 'M. armoricus MXMAG1'. As expected, Ca. 'Methanomassiliicoccus armoricus MXMAG1' had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the 'free-living' clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.

Genetic Plasticity and Ethylmalonyl Coenzyme A Pathway during Acetate Assimilation in Rhodospirillum rubrum S1H under Photoheterotrophic Conditions

Purple nonsulfur bacteria represent a promising resource for biotechnology because of their great metabolic versatility. Rhodospirillum rubrum has been widely studied regarding its metabolism of volatile fatty acid, mainly acetate. As the glyoxylate shunt is unavailable in Rs. rubrum, the citramalate cycle pathway and the ethylmalonyl-coenzyme A (CoA) pathway are proposed as alternative anaplerotic pathways for acetate assimilation. However, despite years of debate, neither has been confirmed to be essential. Here, using functional genomics, we demonstrate that the ethylmalonyl-CoA pathway is required for acetate photoassimilation. Moreover, an unexpected reversible long-term adaptation is observed, leading to a drastic decrease in the lag phase characterizing the growth of Rs. rubrum in the presence of acetate. Using proteomic and genomic analyses, we present evidence that the adaptation phenomenon is associated with reversible amplification and overexpression of a 60-kb genome fragment containing key enzymes of the ethylmalonyl-CoA pathway. Our observations suggest that a genome duplication and amplification phenomenon is not only involved in adaptation to acute stress but can also be important for basic carbon metabolism and the redox balance.IMPORTANCE Purple nonsulfur bacteria represent a major group of anoxygenic photosynthetic bacteria that emerged as a promising resource for biotechnology because of their great metabolic versatility and ability to grow under various conditions. Rhodospirillum rubrum S1H has notably been selected by the European Space Agency to colonize its life support system, called MELiSSA, due to its capacity to perform photoheterotrophic assimilation of volatile fatty acids (VFAs), mainly acetate. VFAs are valuable carbon sources for many applications, combining bioremediation of contaminated environments with the generation of added-value products. Acetate is one of the major volatile fatty acids generated as a by-product of fermentation processes. In Rs. rubrum, purple nonsulfur bacteria, the assimilation of acetate is still under debate since two different pathways have been proposed. Here, we clearly demonstrate that the ethylmalonyl-CoA pathway is the major anaplerotic pathway for acetate assimilation in this strain. Interestingly, we further observed that gene duplication and amplification, which represent a well-known phenomenon in antibiotic resistance, also play a regulatory function in carbon metabolism and redox homeostasis.

Microbial communities of biomethanization digesters fed with raw and heat pre-treated microalgae biomasses

Microalgae biomasses are considered promising feedstocks for biofuel and methane productions. Two Continuously Stirred Tank Reactors (CSTR), fed with fresh (CSTR-C) and heat pre-treated (CSTR-T) Chlorella biomass were run in parallel in order to determine methane productions. The methane yield was 1.5 times higher in CSTR-T with regard to CSTR-C. Aiming to understand the microorganism roles within of the reactors, the sludge used as an inoculum (I), plus raw (CSTR-C) and heat pre-treated (CSTR-T) samples were analyzed by high-throughput pyrosequencing. The bacterial communities were dominated by Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes. Spirochaetae and Actinobacteria were only detected in sample I. Proteobacteria, mainly Alfaproteobacteria, were by far the dominant phylum within of the CSTR-C bioreactor. Many of the sequences retrieved were related to bacteria present in activated sludge treatment plants and they were absent after thermal pre-treatment. Most of the sequences affiliated to the Bacteroidetes were related to uncultured groups. Anaerolineaceae was the sole family found of the Chloroflexi phylum. All of the genera identified of the Firmicutes phylum carried out macromolecule hydrolysis and by-product fermentation. The proteolytic bacteria were prevalent over the saccharolytic microbes. The percentage of the proteolytic genera increased from the inoculum to the CSTR-T sample in a parallel fashion with an available protein increase owing to the high protein content of Chlorella. To relate the taxa identified by high-throughput sequencing to their functional roles remains a future challenge.