Microbial Community Metabolism Research Articles

Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sediments

Abstract. Complex microbial communities facilitate iron and methane transformations in anoxic methanic sediments of freshwater lakes, such as Lake Kinneret (the Sea of Galilee, Israel). The phylogenetic and functional diversity of these consortia are not fully understood, and it is not clear which lineages perform iron reduction and anaerobic oxidation of methane (AOM). Here, we investigated microbial communities from both natural Lake Kinneret iron-rich methanic sediments (>20 cm depth) and iron-amended slurry incubations from this zone using metagenomics, focusing on functions associated with iron reduction and methane cycling. Analyses of the phylogenetic and functional diversity indicate that consortia of archaea (mainly Bathyarchaeia, Methanomicrobia, Thermoplasmata, and Thermococci) and bacteria (mainly Chloroflexi (Chloroflexota), Nitrospirae (Nitrospirota), and Proteobacteria) perform key metabolic reactions such as amino acid uptake and dissimilation, organic matter fermentation, and methanogenesis. The Deltaproteobacteria, especially Desulfuromondales (Desulfuromonadota), have the potential to transfer electrons extracellularly either to iron mineral particles or to microbial syntrophs, including methanogens. This is likely via transmembrane cytochromes, outer-membrane hexaheme c-type cytochrome (OmcS) in particular, or pilin monomers (PilA), all of which were attributed to this lineage. Bona fide anaerobic oxidizers of methane (ANME) and denitrifying methanotrophs Methylomirabilia (NC10) may mediate AOM in these methanogenic sediments; however we also consider the role of methanogens in active AOM or back flux of methanogenesis. Putative aerobes, such as methane-oxidizing bacteria Methylomonas and their methylotrophic syntrophs Methylotenera, are found among the anaerobic lineages in Lake Kinneret iron-amended slurries and are also involved in the oxidation of methane or its intermediates, as suggested previously. We propose a reaction model for the metabolic interactions in these sediments, linking the potential players that interact via intricate metabolic tradeoffs and direct electron transfer between species. Our results highlight the metabolic complexity of microbial communities in an energy-limited environment, where aerobe and anaerobe communities may co-exist and facilitate AOM as one strategy for survival.

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus–host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

Conducting research on diet-microbiome interactions: A review of current challenges, essential methodological principles, and recommendations for best practice in study design.

Diet is one of the strongest modulators of the gut microbiome. However, the complexity of the interactions between diet and the microbial community emphasises the need for a robust study design and continued methodological development. This review aims to summarise considerations for conducting high-quality diet-microbiome research, outline key challenges unique to the field, and provide advice for addressing these in a practical manner useful to dietitians, microbiologists, gastroenterologists and other diet-microbiome researchers. Searches of databases and references from relevant articles were conducted using the primary search terms 'diet', 'diet intervention', 'dietary analysis', 'microbiome' and 'microbiota', alone or in combination. Publications were considered relevant if they addressed methods for diet and/or microbiome research, or were a human study relevant to diet-microbiome interactions. Best-practice design in diet-microbiome research requires appropriate consideration of the study population and careful choice of trial design and data collection methodology. Ongoing challenges include the collection of dietary data that accurately reflects intake at a timescale relevant to microbial community structure and metabolism, measurement of nutrients in foods pertinent to microbes, improving ability to measure and understand microbial metabolic and functional properties, adequately powering studies, and the considered analysis of multivariate compositional datasets. Collaboration across the disciplines of nutrition science and microbiology is crucial for high-quality diet-microbiome research. Improvements in our understanding of the interaction between nutrient intake and microbial metabolism, as well as continued methodological innovation, will facilitate development of effective evidence-based personalised dietary treatments.

Aerobic granular sludge systems for treating hypersaline pharmaceutical wastewater: Start-up, long-term performances and metabolic function

The complex organics, residue pharmaceuticals and high salinity in pharmaceutical wastewater pose great challenges to biological wastewater treatment. In this study, granular sludge process was used for treating pharmaceutical wastewater because of its high pollutant removal efficiency. The results suggested that granules could not form within 90-d cultivation when directly fed with target hypersaline pharmaceutical wastewater (RP) due to suppression of EPS secretion by high concentration of inhibitory organics, while granules were successfully developed with hypersaline synthetic wastewater (RS) and diluted pharmaceutical wastewater (RD), respectively. Further comparison of pollutant removal performance from target pharmaceutical wastewater showed that simultaneous removal of organics (effluent bCOD<1 mg L-1) and nitrogen (average TN removal efficiency of 70.3%) could be achieved in RD. Nevertheless, long acclimation period (i.e., 20 d) was needed for granules when carbon source was shifted from simple sodium acetate to complex organic pollutants in pharmaceutical wastewater, with nitrite significantly accumulated in RS. Analysis of microbial community and nitrogen metabolism pathway indicated the higher abundance of nitrite oxidoreductase than that in the RS to alleviate nitrite accumulation in the RD, and functional strains such as Paracoccus and Mycobacterium played critical roles for high efficiency of organic degradation, nitrification and denitrification.

Novel insight into physicochemical and flavor formation in naturally fermented tilapia sausage based on microbial metabolic network

The quality and flavor formation in fermented fish sausages are based on the complex metabolism of microbial community. In this study, the dynamic changes of physicochemical characteristics, volatile compounds, and microbial communities in the naturally fermented tilapia sausage were studied during the fermentation process. The main physical indexes (gel strength, whiteness, and hardness), dominant flavor free amino acids (glycine, alanine, and glutamic acid) and characteristic volatile flavor compounds (hexanal, heptanal, octanal, benzaldehyde, (E)-2-octenal, 4-ethylbenzaldehyde, (E)-2-heptenal, (E,E)-2,4-decadienal, 1-octen-3-ol, 2-pentylfuran, and 2-ethyl-furan) were significantly enhanced after fermentation, and were positively correlated with Lactococcus, Pediococcus, Enterococcus, and Lactobacillus. The microbial metabolic network showed that Lactococcus, Pediococcus, and Enterococcus played a significant role in the formation of physicochemical and flavor characteristics, while the accumulation of biogenic amines might result from the metabolism of Enterococcus, Enterobacter, and Citrobacter. Isolation of lactic acid bacteria in Lactococcus and Pediococcus might be suitable to improve the fermented tilapia sausage. Microbial metabolic network has revealed the physicochemical and flavor formation of tilapia sausage and can provide guidance for future research on screening of starters.

Examination of hydrogen cross-feeders using a colonic microbiota model

BackgroundHydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing.ResultsAn existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version.ConclusionsAlthough the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.

Mechanistic models of microbial community metabolism.

Microbial communities affect many facets of human health and well-being. Naturally occurring bacteria, whether in nature or the human body, rarely exist in isolation. A deeper understanding of the metabolic functions of these communities is now possible with emerging computational models. In this review, we summarize frameworks for constructing mechanistic models of microbial community metabolism and discuss available algorithms for model analysis. We highlight essential decision points that greatly influence algorithm selection, as well as model analysis. Polymicrobial metabolic models can be utilized to gain insights into host-pathogen interactions, bacterial engineering, and many more translational applications.

Microbial Carbon Metabolic Functions in Sediments Influenced by Resuspension Event

Microorganisms in sediments are an important part of the aquatic ecosystem, and their functional activities are sensitive to external environmental pressure. Shallow lakes are characterized by frequent sediment resuspension events, leading to large amounts of nutrients being released. However, information about the potential impacts of sediment resuspension events on the functional activities of microbial communities is limited. In this study, the responses of microbial carbon metabolism in sediments under different wind–wave disturbance were analyzed by BIOLOG ECO microplates. The results showed that under four disturbance conditions (wind speeds of 0, 1.60, 3.62, and 14.10 m/s), the total carbon metabolism function of the sediment microbial community (represented as average well-color development, AWCD) remained unchanged (p &gt; 0.05), and the final total AWCD value stabilized at about 1.70. However, compared with the control group, some specific carbon sources (e.g., amines and carboxylic acids) showed significant changes (p &lt; 0.05). We found that short-term (8 h) resuspension events did not affect the total carbon metabolism of sediment microbial communities, while it affected the microbial utilization ability of some specific types of carbon sources. For example, we found that the microbial utilization capacity of polymers in the 14.10 m/s group was the best. This study provides a new insight into the carbon cycle process of shallow lake sediments that resuspension events will affect the carbon cycle process of sediments.

Recovery of gut microbiota in mice exposed to tetracycline hydrochloride and their correlation with host metabolism

Antibiotics can disturb the gut microbial community and host metabolism. However, their recovery after antibiotics exposure needs to be characterized, and the correlation between gut microbiota and host metabolism remains unclear. In this study, mice were exposed to 0.5, 1.5 and 10 g/L tetracycline hydrochloride (TET) for 2 weeks, then recovered without TET for another 2 weeks. The results showed that 2-week TET exposure changed microbial community and functions in the mouse gut, and increased abundance of antibiotic resistance genes (ARGs), especially in the 10 g/L TET group. After a 2-week recovery, these changes could only be recovered to the control level in the 0.5 g/L TET exposure group, except for ARGs. Besides gut microbiota, TET exposure also changed metabolic profiles in mouse urine. The 2-week recovery significantly reduced changes in metabolic profiles. Some altered metabolites were found to have a very high correlation with gut microbial community and functions, indicating that TET exposure might induce certain changes in urinary metabolic profiles by altering the gut microbiota. The results from this study suggest that the influences of low-level TET exposure are reversible, except for ARGs, which should be paid more attention. During the application of TET, their dosage should be effectively considered and controlled.

Multiple sugars promote microbial interactions in Chinese baijiu fermentation

The utilization of fermentable sugars determines the succession and metabolism of microbial communities in traditional food fermentations. However, the profile of fermentable sugars and their effects on the microbial interactions and metabolism remains poorly understood. In this study, we revealed the compositions of fermentable sugars in the baijiu fermentation, including maltose, cellobiose, glucose, d-galactose and arabinose. Furthermore, we found the specific sugars (glucose and maltose) were positively correlated with the growth of the abundant genera Lactobacillus and Saccharomyces in the baijiu fermentation. Moreover, a proper combination of sugars mixture (glucose and maltose in a ratio of 9:1, wt/wt) enhanced the symplastic growth and interactions of Lactobacillus and Saccharomyces strains in a simulative baijiu fermentation under the laboratory. Meanwhile, the biomass of Lactobacillus and Saccharomyces strains in the cultivation by the optimized sugars combination were 1.21- and 1.19-fold higher than that of cultivation by the single substrate-sugar. In addition, the formation of these sugars were associated with the saccharifying enzymes from Jiuqu, like GH13 (alpha-amylase, EC 3.2.1.1), GH15 (glucoamylase, EC 3.2.1.3) and so on. This study indicated that specific sugars in substrate-sugars promoted the microbial interactions in baijiu fermentation.

Differential Carbon Utilization by Bacteria in the Soil Surrounding and on Swine Carcasses with Dipteran Access Delayed

Mass mortality events can saturate an environment with decomposing remains. We lack an understanding of such perturbations and the extent of disruption imposed on the local ecosystem. During such instances, normal patterns of colonization and decomposition of remains by necrophagous arthropods can be retarded resulting in delayed colonization due to the proximity of multiple corpses. Therefore, this study was initiated to investigate the impact of carcasses in close proximity with delayed arthropod access on the associated microbial metabolic community profiles and those in the soil immediately under and adjacent to the remains. Field trials were conducted during the summers of 2013 and 2014 in Texas, USA. Three groups of pig carcasses were accessed: those immediately colonized by dipteran species (i.e., primary invertebrate consumers of carrion) and those experiencing delayed dipteran access by 7 or 14 days. Meteorological data for 2013 showed that the mean temperature was 30.59 ± 7.81 °C, accumulated degree hours (ADH) was 30,131.50, and precipitation was 39.12 mm, while in 2014, the mean temperature was 29.27 ± 6.49 °C, ADH was 28,090.70, and total precipitation was 171.45 mm. Bacterial function on the remains in terms of carbon utilization was significantly different between the years as well as between carcass groups, suggesting an inter-kingdom correlation between bacteria and dipteran activity. In contrast, microbial function in the soil was inconsistent between trials, indicating stochasticity within the system, probably due to differences in abiotic factors such as temperature, ADH, and rainfall.

Effects of warming and CO2 enrichment on O2 consumption, porewater oxygenation and pH of subtidal silt sediment

We investigated the effects of seawater warming and CO2 enrichment on the microbial community metabolism (using O2 consumption as a proxy) in subtidal silt sediment. Intact sediment cores, without large dwelling infauna, were incubated for 24 days at 12 (in situ) and 18 °C to confirm the expected temperature response. We then enriched the seawater overlying a subset of cold and warm-incubated cores with CO2 (+ ΔpCO2: 253–396 µatm) for 16 days and measured the metabolic response. Warming increased the depth-integrated volume-specific O2 consumption (Rvol), the maximum in the volume-specific O2 consumption at the bottom of the oxic zone (Rvol,bmax) and the volume-specific net O2 production (Pn,vol), and decreased the O2 penetration depth (O2-pd) and the depth of Rvol,bmax (depthbmax). Benthic photosynthesis oscillated the pH in the upper 2 mm of the sediment. CO2 enrichment of the warm seawater did not alter this oscillation but shifted the pH profile towards acidity; the effect was greatest at the surface and decreased to a depth of 12 mm. Confoundment rendered the CO2 treatment of the cold seawater inconclusive. In warm seawater, we found no statistically clear effect of CO2 enrichment on Rvol, Rvol,bmax, Pn,vol, O2-pd, or depthbmax and therefore suspect that this perturbation did not alter the microbial community metabolism. This confirms the conclusion from experiments with other, contrasting types of sediment.

Single and combined toxicity of the pesticides abamectin and difenoconazole on soil microbial activity and Enchytraeus crypticus population

Besides being toxic to enchytraeids, pesticides may also affect microbial communities, which are the main diet of enchytraeids. This study aimed to analyze the individual and combined effects of the insecticide Kraft® 36 EC (abamectin) and the fungicide Score® 250 EC (difenoconazole) to soil microbial communities and Enchytraeus crypticus populations. The abamectin and difenoconazole effects to the microbial community metabolism, as revealed by qCO2 increase in the first two periods of exposure, might indicate an acute effect of pesticides, which might result in lowered microbial biomass once microorganisms spend more energy in detoxification processes than in microbial growth. E. crypticus juvenile production was not affected at the different conditions tested. However, the importance of microorganisms on the enchytraeids diet was ratified. Besides, it is important to emphasize that only one recommended dose of the pesticides was tested in this study. Hence, other situations (e.g. pesticides over application or a slower process of pesticides degradation) may result in a different scenario of effects and should be further investigated.

Effect of Azamethiphos on enzymatic activity and metabolic fingerprints of marine microbial communities from the water column

Salmon production in Chile has increased significantly since the 1990s. However, there have been significant economic losses owing to outbreaks of Caligus rogercresseyi. Pesticides, among them Azamethiphos, are used to mitigate the impact of this sea louse. Azamethiphos can affect non-target species living near salmon farms such as microbial plankton, although there is little information about this. The general objective of this study was to determine the effect of different concentrations of the pesticide Azamethiphos on the metabolism of microbial plankton communities (<100 μm) in two contrasting zones, one without salmon farming and the other with a high level of aquaculture activity. Several methodological approaches were used, including the enzymatic activity of β-glucosidase and malate dehydrogenase (MDH), fingerprinting techniques (EcoPlates for bacteria and FF microplate for marine fungi) and the estimation of microbial aerobic respiration. We found greater degradation of the pesticide Azamethiphos in the salmon culture zone (~72.4%) than in an area not previously used in salmon production (~26.1%). The response of microbial β-glucosidase activity to Azamethiphos is highly variable, but there is a tendency toward more activity in the smaller size fractions (5–25 μm and 0.22–3 μm) when exposed to high Azamethiphos concentrations. We also detected a highly variable response in microbial MDH activity. The most widely used carbon substrates by bacterioplankton and marine fungi are those related to carbohydrate metabolism. We also found increased use of carboxylic acids and amino acids in the treatments with higher concentrations of Azamethiphos. Enzyme activity, together with metabolic fingerprints, could be used as an indicator of perturbations in marine microbial communities.

Impacts of carbon-based nanomaterials on nutrient removal in constructed wetlands: Microbial community structure, enzyme activities, and metabolism process

The increasing use of raw carbon-based nanomaterials (CBNs) will inevitably affect wastewater treatment systems. Constructed wetlands (CWs) are ecological wastewater treatment facilities and can intercept the vast particles pollutant, including CBNs. However, the impacts of CBNs on the treatment performance of CWs have no available knowledge. Therefore, we systematically inspected the effects of single-walled and multi-walled carbon nanotubes (SWCNTs and MWCNTs) and fullerene nanoparticles (C60) on CW performance under 180-day exposure to 0, 10 and 1000 μg/L concentrations. The results showed that CBNs had marginally adverse impacts on chemical oxygen demand (COD) and total phosphorus (TP) removal, whereas nitrogen removal declined by 24.1 %–42.7 % following long-term exposure to CBNs. MWCNTs had the greatest inhibition effect on nitrogen removal, followed by SWCNTs and C60. The CBNs also induced reactive oxygen species (ROS) overproduction as the increasing concentration, which confirmed that CBNs have biotoxic effects in CWs. The variation of functional microbial community and the inhibition of enzyme activities were the dominant reasons for the decline in nitrogen removal efficiency. Furthermore, predictive functional profiling showed that CBNs affected functional gene abundance, and caused a decline in the enzymes abundance connected to nitrogen removal by the end of the 180-day exposure period.

Soil organic matter dynamics and microbial metabolism along an altitudinal gradient in Highland tropical forests

The highland forests of tropical regions are highly vulnerable to climate change because changes in soil organic quality due to the increased soil water deficit conditions through rising temperatures. Several authors have reported that labile molecules dominate soil organic matter at higher elevations, and it is therefore more vulnerable to the rising temperatures associated with climate change. The objective of the present study was to analyze the effect of interaction between the chemical composition of organic matter derived from the dominant plant species and the metabolism of microbial community along an elevational gradient in a highland forest in Central Mexico. The study compared three vegetation-soil systems that represent three different elevational levels: Alnus-system (3100 m.a.s.l.), Abies-system (3500 m.a.s.l.) and Pinus-system (3700 m.a.s.l.). The SOM produced in the lowest site is more recalcitrant (i.e., higher Alkyl:O-Alkyl ratio) as a result of the lower water availability than in the highest site. The results of Threshold Elemental RatioC:N (TERC:N) and TERC:P for the organic layer were lower than their C:N and C:P ratios in the organic layer, supporting that the microbial community of the organic layer in the site of lowest elevation must be limited by the carbon source, rather than by N and P. However, these results were not found in the mineral soil, suggesting that the drivers of organic matter decomposition differ between the organic layer and the mineral soil. As a conclusion, our results suggest that the chemical recalcitrance of organic matter (at the lowest site) and temperature (at the highest site) reduce the microbial metabolic activity in the forest floor. Integrated study of plant-derived organic material and the microbial metabolism of the forest floor is therefore required to achieve a full understanding of the vulnerability of tropical mountain ecosystems to climate change.

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

BackgroundViruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and assessing their metabolic impacts on microbiomes.DesignHere we present VIBRANT, the first method to utilize a hybrid machine learning and protein similarity approach that is not reliant on sequence features for automated recovery and annotation of viruses, determination of genome quality and completeness, and characterization of viral community function from metagenomic assemblies. VIBRANT uses neural networks of protein signatures and a newly developed v-score metric that circumvents traditional boundaries to maximize identification of lytic viral genomes and integrated proviruses, including highly diverse viruses. VIBRANT highlights viral auxiliary metabolic genes and metabolic pathways, thereby serving as a user-friendly platform for evaluating viral community function. VIBRANT was trained and validated on reference virus datasets as well as microbiome and virome data.ResultsVIBRANT showed superior performance in recovering higher quality viruses and concurrently reduced the false identification of non-viral genome fragments in comparison to other virus identification programs, specifically VirSorter, VirFinder, and MARVEL. When applied to 120,834 metagenome-derived viral sequences representing several human and natural environments, VIBRANT recovered an average of 94% of the viruses, whereas VirFinder, VirSorter, and MARVEL achieved less powerful performance, averaging 48%, 87%, and 71%, respectively. Similarly, VIBRANT identified more total viral sequence and proteins when applied to real metagenomes. When compared to PHASTER, Prophage Hunter, and VirSorter for the ability to extract integrated provirus regions from host scaffolds, VIBRANT performed comparably and even identified proviruses that the other programs did not. To demonstrate applications of VIBRANT, we studied viromes associated with Crohn’s disease to show that specific viral groups, namely Enterobacteriales-like viruses, as well as putative dysbiosis associated viral proteins are more abundant compared to healthy individuals, providing a possible viral link to maintenance of diseased states.ConclusionsThe ability to accurately recover viruses and explore viral impacts on microbial community metabolism will greatly advance our understanding of microbiomes, host-microbe interactions, and ecosystem dynamics.7uVs82Bc4tfSLymdHQuU_3Video

ASLO 2020 Award Winners

<scp>ASLO</scp> 2020 Award Winners

Hygienization and microbial metabolic adaptation during anaerobic co-digestion of swine manure and corn stover

This study assessed the effect of different swine manure (SM)/corn stover (CS) mixtures based on total solids (TS) content with respect to hygienization, microbial community dynamics and methane yields on batch anaerobic co-digestion performance. Different ratios of SM and CS with TS content between 0.69 and 6% digested at 75 d revealed SM had the greatest methane yield at 403.9 mL g−1 volatile solids added (VS) and 86.31% VS reduction. BIOLOG AN microplates and lignocellulolytic enzyme assays proved to be rapid tools for characterizing microbial community metabolism as noted by the different carbon source utilization patterns between TS loadings. Hygienization of fecal indicator bacteria groups was achieved with some (E. coli) but not all groups (Clostridia spp.). The results showed that colorimetric biochemical assays and culture-based techniques can rapidly assess microbial community dynamics during co-digestion, and that TS- in the form of lignocellulosic biomass- influences microbial metabolic activities.

Ecological diversity, evolution and metabolism of microbial communities in the wet fermentation of Australian coffee beans

The microbial ecology in the fermentation of Australian coffee beans was investigated in this study. Pulped coffee beans were kept underwater for 36 h before air dried. Samples were collected periodically, and the microbial communities were analyzed by culture-dependent and independent methods. Changes in sugars, organic acids and microbial metabolites in the mucilage and endosperm of the coffee beans during fermentation were monitored by HPLC. Culture-dependent methods identified 6 yeast and 17 bacterial species, while the culture-independent methods, multiple-step total direct DNA extraction and high throughput sequencing, identified 212 fungal and 40 bacterial species. Most of the microbial species in the community have been reported for wet fermentation of coffee beans in other parts of the world, but the yeast Pichia kudriavzevii was isolated for the first time in wet coffee bean fermentation. The bacterial community was dominated by aerobic mesophilic bacteria (AMB) with Citrobacter being the predominant genus. Hanseniaspora uvarum and Pichia kudriavzevii were the predominant yeasts while Leuconostoc mesenteroides and Lactococcus lactis were the predominant LAB. The yeasts and bacteria grew significantly during fermentation, utilizing sugars in the mucilage and produced mannitol, glycerol, and lactic acid, leading to a significant decrease in pH. The results of this study provided a preliminary understanding of the microbial ecology of wet coffee fermentation under Australian conditions. Further studies are needed to explore the impact of microbial growth and metabolism on coffee quality, especially flavour.