Dominant Microbial Groups Research Articles

Microbial community structure and function in a sandy soil column under dynamic hydrologic regimes

The capillary fringe (CF) exhibits steep chemical and redox gradients, representing a critical reactive interface in the subsurface. The spatial extent of the CF is temporally dynamic because of water table and soil moisture fluctuations. To simulate the spatio-temporal responses of the CF’s microbial community structure and activity, a 91 cm long sandy soil column experiment was conducted by imposing three different sequential hydrologic regimes: a stable water table separating the unsaturated and saturated zones (static regime), periodic pulse infiltration events with a constant water table position (infiltration regime), and water table fluctuations under three drainage-imbibition cycles of 6, 12, and 18 days (fluctuating regime). The investigation focused on the microbially-mediated turnover of nitrogen (N) and carbon (C). Geochemical profiles in the soil column were monitored continuously, while microbial DNA was extracted for 16S rDNA sequencing at the start, middle and end of the experiment. The observed microbial community compositions corresponded to five categories: (1) initial soil, (2) near-surface and (3) CF and saturated soil under the infiltration regime, (4) unsaturated and (5) saturated soil in the fluctuating regime. Based on co-occurrence network analysis, microbial physiologies matched the predominant geochemical conditions, and relatively stable community structures prevailed throughout the experiment. NO3- and NH4+ were more available to the microbes in the fluctuating regime’s alternating oxic/anoxic zone, leading to a more flexible network. The prevalent microbial metabolic pathways predicted using FAPROTAX were mainly associated with N and C metabolisms and significantly correlated with the taxonomic compositions. However, the dominant microbial groups were shared among all the soil samples. The limited spatial differences in microbial community structure under the fluctuating regime were likely due to a more pronounced role of microbial activity than microbial diversity, and similar drying-wetting conditions between the soil column and the filed site. Internally consistent geochemical and microbial depth stratifications were identified by (1) the redox potential and nitrogen species distributions, (2) spatial moment analysis of NO3- and NH4+ concentrations, (3) microbial community composition and (4) function. The five imposed hydrologic regimes generated distinct and coupled geochemical and microbial signatures. These signatures resulted from variations in the soil microbial community’s activity, rather than diversity or abundance.

Elucidating Key Microbial Drivers for Methane Production during Cold Adaptation and Psychrophilic Anaerobic Digestion of Cattle Manure and Food Waste

At psychrophilic temperatures (<20 °C), anaerobic digestion produces less methane (CH4). For psychrophilic anaerobic digestion (PAD) to be successful, investigation of cold-adapted microbial consortia involved in methane production is critical. This study aimed to investigate the microbial community driving enhanced methane production from the cold-adaptation process and bioaugmentation of PAD with cold-adapted inoculum (BI). Microbial consortia in cattle manure (CM) and food waste (FW) were adapted and applied during batch PAD of CM and FW to bioaugment methane production at 15 °C. Cold adaptation and PAD with BI resulted in cumulative specific methane yields of 0.874 ± 0.231 and 0.552 ± 0.089 L CH4 g−1 volatile solids, respectively, after 14 weeks, while the absence of BI (control) led to acidification and no methane production during PAD. Following 16S rRNA V4–V5 amplicon sequencing and metagenomic analyses, Methanosarcina was revealed as a key driver of methanogenesis during cold adaptation and PAD bioaugmentation. Furthermore, based on the predictive functional and metabolic analysis of the communities, possible synergies were proposed in terms of substrate production and utilization by the dominant microbial groups. For instance, during methane production, Bacteroides and Methanobrevibacter were possibly involved in a syntrophic relationship, which promoted methanogenesis by Methanosarcina. These findings provide insight into the prospective microbial synergies that can be harnessed and/or regulated in cold-adapted inoculum for the improvement of methane production during PAD.

Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities.

Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.

The comparative plastisphere microbial community profile at Kung Wiman beach unveils potential plastic-specific degrading microorganisms.

Plastic waste is a global environmental issue that impacts the well-being of humans, animals, plants, and microorganisms. Microplastic contamination has been previously reported at Kung Wiman Beach, located in Chanthaburi province along with the Eastern Gulf of Thailand. Our research aimed to study the microbial population of the sand and plastisphere and isolate microorganisms with potential plastic degradation activity. Plastic and sand samples were collected from Kung Wiman Beach for microbial isolation on agar plates. The plastic samples were identified by Fourier-transform infrared spectroscopy. Plastic degradation properties were evaluated by observing the halo zone on mineral salts medium (MSM) supplemented with emulsified plastics, including polystyrene (PS), polylactic acid (PLA), polyvinyl chloride (PVC), and bis (2-hydroxyethyl) terephthalate (BHET). Bacteria and fungi were identified by analyzing nucleotide sequence analysis of the 16S rRNA and internal transcribed spacer (ITS) regions, respectively. 16S and ITS microbiomes analysis was conducted on the total DNA extracted from each sample to assess the microbial communities. Of 16 plastic samples, five were identified as polypropylene (PP), four as polystyrene (PS), four as polyethylene terephthalate (PET), two as high-density polyethylene (HDPE), and one sample remained unidentified. Only 27 bacterial and 38 fungal isolates were found to have the ability to degrade PLA or BHET on MSM agar. However, none showed degradation capabilities for PS or PVC on MSM agar. Notably, Planococcus sp. PP5 showed the highest hydrolysis capacity of 1.64 ± 0.12. The 16S rRNA analysis revealed 13 bacterial genera, with seven showing plastic degradation abilities: Salipiger, Planococcus, Psychrobacter, Shewanella, Jonesia, Bacillus, and Kocuria. This study reports, for the first time of the BHET-degrading properties of the genera Planococcus and Jonesia. Additionally, The ITS analysis identified nine fungal genera, five of which demonstrated plastic degradation abilities: Aspergillus, Penicillium, Peacilomyces, Absidia, and Cochliobolus. Microbial community composition analysis and linear discriminant analysis effect size revealed certain dominant microbial groups in the plastic and sand samples that were absent under culture-dependent conditions. Furthermore, 16S and ITS amplicon microbiome analysis revealed microbial groups were significantly different in the plastic and sand samples collected. We reported on the microbial communities found on the plastisphere at Kung Wiman Beach and isolated and identified microbes with the capacity to degrade PLA and BHET.

Dominance by cyanobacteria in the newly formed biofilms on stone monuments under a protective shade at the Beishiku Temple in China

Following the installation of a protective shade, rapid propagation of microorganisms showing in black and grey colors occurred at Beishiku Temple in Gansu Province of China. This study employed a combination of high-throughput sequencing technology, morphological examinations, and an assessment of the surrounding environmental condition to analyze newly formed microbial disease spots. The investigation unveiled the responsible microorganisms and the instigating factors of the microbial outbreak that subsequently to the erection of the shade. Through comparison of bioinformatics, the ASV method surpasses the OTU method in characterizing community compositional changes by the dominant microbial groups, the phylum Cyanobacteria emerged as the most dominant ones in the microbial community accountable for the post-shade microbial deterioration. The black spot and grey spot are predominantly composed of Mastigocladopsis and Scytonema, respectively. Validation analysis, based on the active RNA-level community results, supported and validated these conclusions. Comparative scrutiny of the microbial community before shade installation and the background environmental data disclosed that the erection of the shade prompted a decrease in temperatures and an increase in humidity within the protected area. Consequently, this spurred the exponential proliferation of indigenous cyanobacteria in the spots observed. The outcomes of this study carry considerable significance in devising preventive conservation strategies for cultural heritage and in managing the process of biodeterioration.

Comparative Analysis of Chemical, Microbiological, Sensory and Volatile Compound Profiles in Manouri PDO and Artisanal Manouri Cheeses: A Preliminary Study

Manouri, a protected designation of origin (PDO) cheese, is one of the most popular whey cheeses produced in Greece. The objective of the current study was to investigate if there are differences between artisanal and industrial Manouri cheeses regarding microbiological quality, volatile organic compounds (VOCs) profile and other quality parameters (colour, texture), sensory attributes and spectral characteristics detected by Fourier transform infrared spectroscopy (FT-IR) that may discriminate the samples. Differences were detected in the population of the dominant microbial groups, especially for lactic acid bacteria (LAB), Enterobacteriaceae and yeast counts. No discrimination was attained from the physicochemical analyses, except for the pH values. A total of 50 VOCs were identified, including ketones, lactones, free fatty acids, aldehydes, esters, alcohols and hydrocarbons. Sensory evaluation was carried out using a quantitative descriptive analysis (QDA) panel and a consumer panel. Consumers showed a preference for the artisanal Manouri, and the QDA panel revealed significant differences in 11 out of the 17 sensory attributes. Colour and texture analyses were also performed and showed specific differences in yellowness, as well as in fracturability and hardness. FT-IR spectral analysis demonstrated potential discrimination related to the phospholipid content and profile of artisanal and industrial Manouri.

Linking Topographical Ring Features to Geochemical and Geophysical Anomalies

Circular features in forests seen from air have been studied for several decades at different locations around the world. Forest rings, as they are called in Canada’s boreal forests, express several geochemical (pH, carbonate content) and geophysical (surface potential) anomalies on their 20–30 m wide ring edges. Although it has been proposed that microbial processes may cause these anomalies, the exact mechanisms of ring formation are still unknown. We focused on the Thorn North forest ring in Ontario, Canada to correlate the surface potential anomaly to soil gas concentrations. Field measurements showed that the surface potential drop at the ring edge center is framed by peaks in CO2 production, which is linked to O2 depletion and methane generation. Carbon isotope signatures were found to drop to lighter values (down to −20‰), suggesting increased respiration. Higher concentrations of uronic acids bound to extracellular polymeric substances were found, indicating that the surface potential anomaly is linked to respiration. 16S rRNA gene sequencing of shallow soil did not indicate a dominant microbial group on the edges; instead, principal component analysis showed that the microbial composition was controlled by the substrate (clayey vs. sandy soil), therefore future studies should focus on deeper ground layers.

Brine Volatilome Changes Along the Spontaneous Fermentation of Spanish-Style cv. Chalkidiki Green Olives Under High and Low NaCl Conditions

Table olives are essential components of the Mediterranean diet. Yet, their contribution to salt intake has prompted efforts to reformulate traditional products via safe interventions, mainly focused on the fermentation step. The volatilomics approach is an important tool to assess the complex table olives fermentation. However, extensive data related to monitoring of volatile organic compounds (VOCs) in manufacturing process of Spanish-style cv. Chalkidiki green table olives are scarce in the literature. The present work systematically examines VOCs profile in brines during spontaneous fermentation of cv. Chalkidiki olives under high (8% w/v) and 50% lower NaCl content using selected combinations of chloride salts (NaCl, KCl, CaCl2) in pilot scale for two consecutive periods. VOCs were determined by headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry. Changes in the population of the dominant microbial groups, pH, and titratable acidity values were also investigated. A total of 56 VOCs were identified, including acids, alcohols, carbonyls, esters, and phenols. Multivariate data analysis explored the links between volatile metabolites, microbial groups, and fermentation stages under different NaCl conditions. The evolution of propanoic acid and 2-butanol was intriguing for monitoring a fermentation dominated by lactic acid bacteria under low NaCl conditions, while 3-methyl-1-butanol was indicative of yeast prevalence arising from seasonal variation and/or high NaCl processing. Τhe important contribution of acetic acid to the overall VOCs profile at a late fermentation stage was typical in low NaCl brines. The complete results could be beneficial for marker-assisted monitoring of the fermentation processes in the future.

Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters

Biofiltration is used worldwide to provide safe potable water due to its low energy demand and excellent treatment performance. For instance, in Denmark, over 95% of drinking water is supplied through groundwater-fed rapid sand filters (RSF). Bacteriophages, viruses that infect bacteria, have been shown to shape the taxonomic and functional composition of microbial communities across a range of natural and engineering systems. However, phages in the biofiltration systems are rarely studied, despite the central role microbes play in water purification. To probe this, metagenomic data from surface water, groundwater and mixed source water biofiltration units (n = 26 from China, Europe and USA) for drinking water production were analysed to characterize prokaryotic viruses and to identify their potential microbial hosts. The source water type and geographical location are found to exert influence on the composition of the phageome in biofilters. Although the viral abundance (71,676 ± 17,841 RPKM) in biofilters is only 14.4% and 17.0% lower than those of the nutrient-rich wastewater treatment plants and fresh surface waters, the richness (1,441 ± 1,046) and diversity (Inverse Simpson: 91 ± 61) in biofiltration units are significantly less by a factor of 2–5 and 3–4, respectively. In depth analysis of data from 24 groundwater-fed RSFs in Denmark revealed a core phageome shared by most RSFs, which was consistently linked to dominant microbial hosts involved in key biological reactions for water purification. Finally, the high number of specific links detected between phages and bacterial species and the large proportion of lytic phages (77%) led to the conjecture that phages regulate bacterial populations through predation, preventing the proliferation of dominant species and contributing to the established functional redundancy among the dominant microbial groups. In conclusion, bacteriophages are likely to play a significant role in water treatment within biofilters, particularly through interactions with key bacterial species.

Use of a Highly Specialized Biocatalyst to Produce Lactate or Biohydrogen and Butyrate from Agro-Industrial Resources in a Dual-Phase Dark Fermentation

This study aimed at investigating the feasibility of using a highly specialized bacterial inoculum harboring lactic acid bacteria (LAB) and lactate-oxidizing, hydrogen-producing bacteria (LO-HPB) to produce either lactate or biohydrogen and butyrate from several agro-industrial resources via dual-phase dark fermentation. The feedstocks were fruit–vegetable waste, cheese whey, coffee wastewater, tequila vinasse, and maize processing wastewater, and were tested in both mono- and co-fermentation. The results obtained indicated that the biocatalyst used was able to perform a dual-phase lactate fermentation, producing high lactate (13.1–36.4 g/L), biohydrogen (0.2–7.5 NL H2/Lfeedstock, equivalent to 0.3–1.7 mol H2/mol hexose), and butyrate (3.3–13.9 g/L) with all the tested feedstocks. A series of self-fermentation tests were also performed with crude cheese whey and fruit–vegetable waste for comparison purposes. Compared to inoculum-aided fermentations, the self-fermentation exhibited a reduced bioconversion efficiency. Short-length 16S rRNA gene sequencing analysis showed that LO-HPB was the dominant microbial group (86.0%) in the biocatalyst, followed by acetic acid bacteria (5.8%) and LAB (5.7%). As expected, the molecular analysis also showed significant differences in the microbial community structure of the biocatalyst and those that evolved from self-fermentation. Besides lactate fermentation and oxidation, the biocatalyst also assisted the bi-phasic lactate fermentation via oxygen consumption, and apparently, via substrate hydrolysis. Overall, this study can lay the foundation for robust inoculum development, which is of special significance in the field of dark fermentation, and proposes an innovative bioprocess for agro-industrial valorization through a trade-off approach, tailoring the metabolic pathway to the target product(s).

Performances and mechanisms of simultaneous removal of nitrate and phosphate by biofilter assembled with sponge iron/copper and corn cobs

Sponge iron (SI) is a potential material for removing nitrate and phosphate from water. We decorated the SI with copper (Cu) to enhance its removal performance. To gain insight into the nitrate and phosphate removal utilizing SI/Cu and microbial coupling systems, three biofilters filled with corn cob (CC), corn cob + sponge iron (CS) and corn cob + sponge iron/copper (CSCu) were constructed. The results showed that the effluent NO3–-N and PO43−-P concentrations of CSCu remained consistently below 1 and 0.1 mg/L. The introduction of SI/Cu led to the enrichment of the Dechloromonas genus, making it the dominant microbial group, occupying 42.65% of the effective sequences. Modification of SI with Cu increased nitrogen cycle-related functional genes abundance in CSCu, with a 634% increase in nirS compared to CS. These findings proved that SI/Cu was a promising material, providing an approach to concomitantly removing nitrate and phosphate.

Global warming induces the succession of photosynthetic microbial communities in a glacial lake on the Tibetan Plateau

As an important freshwater resource in the Qinghai-Tibet Plateau, glacial lakes are being immensely affected by global warming. Due to the lack of long-term monitoring data, the processes and driving mechanisms of the water ecology of these glacial lakes in a rapidly changing climate are poorly understood. This study, for the first time, reconstructed changes in water temperature and photosynthetic microbial communities over the past 200 years in Lake Basomtso, a glacial lake on the southeastern Tibetan Plateau. Temperatures were reconstructed using a paleotemperature proxy based on branched glycerol dialkyl glycerol tetraethers (brGDGTs), the cell membrane lipids of some bacteria, and photosynthetic microbial communities were determined by high-throughput DNA sequencing. The reconstructed mean annual air temperature (MAAT) at Lake Basomtso varied between 6.9 and 8.3 °C over the past 200 years, with a rapid warming rate of 0.25 °C /10 yrs after 1950s. Carbon isotope of sediment and n-alkane analyses indicate that ≥95% of the organic matter in Lake Basomtso is derived from a mixture of terrestrial C3 plants and endogenous organic matter inputs, and the proportion of endogenous organic matter in the sediments has gradually increased since the 1960s. The sedimentary DNA analyses of the sediment core reveal that Chloracea is the most dominant prokaryotic photosynthetic microbial group (84.5%) over the past 200 years. However, the relative abundance of Cyanobacteria has increased from ≤6.8% before the 1960s to 15.5% nowadays, suggesting that warmer temperatures favor the growth of Cyanobacteria in glacial lakes. Among eukaryotic photosynthetic microorganisms, the Chlorophyceae have been gradually replaced by Dinoflagellata and Diatomacae since the 1980s, although the Chlorophyceae still had the highest average relative abundance overall (30–40%). The Pb isotopic composition, together with the total phosphorous concentration, implies that human activity exerted a minimal impact on Lake Basomtso over the past 200 yrs. However, the synchronous fluctuations of total organic carbon (TOC), total nitrogen (TN), and metal elements in sediments suggest that temperature appears to have a strong influence on nutrient input to Lake Basomtso by controlling glacial erosion. Global warming and the concurrent increase in glacial meltwater are two main factors driving changes in nutrient inputs from terrestrial sources which, in turn, increases the lake productivity, and changes microbial community composition. Our findings demonstrate the sensitive response of glacial lake ecology to global warming. It is necessary to strengthen the monitoring and research of glacial lake ecology on the Tibetan plateau, so as to more scientifically and accurately understand the response process and mechanism of the glacial lake ecosystem under global warming.

Effect of Multiple Rounds of Enrichment on Metabolite Accumulation and Microbiota Composition of Pit Mud for Baijiu Fermentation.

Pit mud (PM) is the main component of Baijiu (traditional Chinese liquor), and its microorganisms are the primary sources of the aroma of Chinese strong-flavor Baijiu (SFB). Enrichment plays an important role in the selection of functional microorganisms in PM. Herein, the PM of SFB was submitted to six rounds of enrichment using clostridial growth medium (CGM), and changes in the metabolite accumulation and microbiota composition were evaluated. Based on the metabolite production and microbiota composition, the enrichment rounds were classified as the acclimation stage (round 2), main fermentation stage (rounds 3 and 4), and late fermentation stage (rounds 5 and 6). Species within the genus Clostridium dominated in the acclimation stage (65.84-74.51%). In the main fermentation stage, the dominant microbial groups were producers of butyric acid, acetic acid, and caproic acid, which included Clostridium (45.99-74.80%), Caproicibacter (1.45-17.02%), and potential new species within the order of Oscillataceae (14.26-29.10%). In the late stage of enrichment, Pediococcus dominated (45.96-79.44%). Thus, the main fermentation stage can be considered optimal for the isolation of acid-producing bacteria from PM. The findings discussed herein support the development and application of functional bacteria by bioaugmentation, and contribute to improving the quality of PM and SFB production.

Combined forage grass-microbial for remediation of strontium-contaminated soil

Enrichment plants were screened from six forage grasses in this study to establish a complete combined forage grass-microbial remediation system of strontium-contaminated soil, and microbial groups were added to the screened dominant forage grasses. The occurrence states of strontium in forage grasses were explored by the BCR sequential extraction method. The results showed that the annual removal rate of Sudan grass (Sorghum sudanense (Piper) Stapf.) reached 23.05% in soil with a strontium concentration of 500 mg·kg−1. Three dominant microbial groups: E, G and H, have shown good facilitation effects in co-remediation with Sudan grass and Gaodan grass (Sorghum bicolor × sudanense), respectively. When compared to the control, the strontium accumulation of forage grasses in kg of soil with microbial groups was increased by 0.5–4 fold. The optimal forage grass-microbial combination can theoretically repair contaminated soil in three years. The microbial group E was found to promote the transfer of the exchangeable state and the reducible state of strontium to the overground part of the forage grass. Metagenomic sequencing results showed that the addition of microbial groups increased Bacillus spp. in rhizosphere soil, enhanced the disease resistance and tolerance of forage grasses, and improved the remediation ability of forage grass-microbial combinations.

Effect of alkali treatment and natural fermentation on the residue behaviour of malathion and malaoxon during table olive production

Pesticide use is indispensable for combating diseases occurring during olive cultivation. However, this has led to challenges of pesticide residues in consumer products as a result of pesticide application errors and the methods used during processing and preservation. This work aimed to identify the effects of table olive processing and preservation techniques on the concentrations of malathion and its degradation product malaoxon. For this purpose, olive trees in an experimental olive orchard were sprayed homogeneously with malathion at a dose of 975 mg L−1 and processed as (i) vacuum-packed, (ii) alkali treated and (iii) directly brined for natural fermentation. The changes in microbial growth, pH-acidity and pesticide (malathion and malaoxon) concentrations were monitored regularly during the experiment. Lactic acid bacteria, yeast and mould growth were not detected in any of the treatments. Mesophilic aerobic bacteria and enterobacteria were the dominant microbial groups in all non-sprayed treatments, but no enterobacteria growth was detected in sprayed treatments. Lower pH values were observed in the brines of natural fermentation treatments of both sprayed and non-sprayed olives. The independent effects of time and processing method and their interactions on malathion and malaoxon concentrations were found significant (p < .05). During the experiments, the highest reduction in malathion concentration was observed in alkali treated samples (95–99%), followed by naturally fermented (77–88%) and vacuum-packed samples (74–76%). Processing factors for all treatments were lower than 1.

Feasibility of successive hydrogen and methane production in a single-reactor configuration of batch anaerobic digestion through bioaugmentation and stimulation of hydrogenase activity and direct interspecies electron transfer

Two-stage anaerobic digestion is a promising way to increase the efficiency of decomposition of organic waste. However, spatial separation of stages makes this technology less economically attractive. In this work, we studied a model of two-stage anaerobic digestion with stages separated in time in one reactor. To implement this model, we used a combination of (1) bioaugmentation with a hydrogen-producing Thermoanaerobacterium thermosaccharolyticum SP-H2, resistant to low pH, (2) setting a low initial pH (5.5) to reduce the activity of hydrogenotrophic methanogens, (3) supplementing additives in the form of soluble iron (II) and granular activated carbon (GAC) to stimulate hydrogenase activity and direct interspecies electron transfer (DIET), respectively. For comparison, two methanogenic inoculums with different dominant microbial groups and initial iron concentrations were used. With the simultaneous addition of GAC and iron (II), sequential production of hydrogen and methane was observed for both methanogenic inoculums. Without the addition of GAC, methane formation was practically not observed, which, apparently, indicated the impossibility of syntrophic degradation of acidogenesis products due to the high partial pressure of hydrogen and the absence of conductive material for activation of DIET. Significant differences in hydrogenase activity and the kinetics of hydrogen and methane formation according to the modified Gompertz equation depending on the iron content in the system may indicate the importance of this additive. Further studies should be aimed at determining the optimal initial pH, concentrations of stimulating additives, bioaugmentation and methanogenic cultures, as well as confirming the stability of the proposed single-reactor two-stage anaerobic digestion system in semi-continuous mode.

Understanding the Effects of Self-Induced Anaerobic Fermentation on Coffee Beans Quality: Microbiological, Metabolic, and Sensory Studies.

In this study, an investigation of the microbial community structure and chemical changes in different layers of a static coffee beans fermentation tank (named self-induced anaerobic fermentation-SIAF) was conducted at different times (24, 48, and 72 h). The microbial taxonomic composition comprised a high prevalence of Enterobacteriaceae and Nectriaceae and low prevalence of lactic acid bacteria and yeast, which greatly differs from the traditional process performed in open tanks. No major variation in bacterial and fungal diversity was observed between the bottom, middle, and top layers of the fermentation tank. On the other hand, the metabolism of these microorganisms varied significantly, showing a higher consumption of pulp sugar and production of metabolites in the bottom and middle layers compared to the top part of the fermentation tank. Extended processes (48 and 72 h) allowed a higher production of key-metabolites during fermentation (e.g., 3-octanol, ethyl acetate, and amyl acetate), accumulation in roasted coffee beans (acetic acid, pyrazine, methyl, 2-propanone, 1-hydroxy), and diversification of sensory profiles of coffee beverages compared to 24 h of fermentation process. In summary, this study demonstrated that SIAF harbored radically different dominant microbial groups compared to traditional coffee processing, and diversification of fermentation time could be an important tool to provide coffee beverages with novel and desirable flavor profiles.

Effects of Invasive Plant Diversity on Soil Microbial Communities

Native plant communities can be invaded by different numbers of alien plant species or by the same number of alien plant species with different levels of evenness. However, little is known about how alien invasive plant species richness and evenness affect soil microbial communities. We constructed native herbaceous plant communities invaded by exotic plants with different richness (1, 2, 4 and 8 species) and evenness (high and low) and analyzed soil physico-chemical properties and the diversity and composition of soil fungal and bacterial communities by high-throughput Illumina sequencing. Overall, the species richness and evenness of invasive plants had no significant effect on bacterial and fungal alpha diversity (OTUs, Shannon, Simpson, Chao1 and ACE) or the soil physico-chemical properties. However, invasive species richness had a significant impact on the relative abundance of the most dominant fungi, Ascomycota and Bipolaris, and the dominant bacteria, Actinobacteriota, which increased with increasing invasive species richness. The relative abundance of the dominant microbial groups was significantly correlated with the relative abundance of some specific invasive plants in the community. This study sheds new light on the effects of plant co-invasion on soil microbial communities, which may help us understand the underlying mechanisms of multiple alien plant invasion processes from the perspective of soil microorganisms.

Exploration of the roles of microbiota on biogenic amines formation during traditional fermentation of Scomber japonicus.

The influence of microbiota composition and metabolisms on the safety and quality of fermented fish products is attracting increasing attention. In this study, the total viable count (TVC), pH, total volatile base nitrogen (TVB-N) as well as biogenic amines (BAs) of traditional fermented Scomber japonicus (zaoyu) were quantitatively determined. To comprehend microbial community variation and predict their functions during fermentation, 16S rRNA-based high-throughput sequencing (HTS) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were employed, respectively. The fresh samples stored without fermentation were used as controls. TVC and TVB-N values increased rapidly, and the content of BAs exceeded the permissible limit on day 2 in the controls, indicating serious spoilage of the fish. In contrast, a slower increase in TVC and TVB-N was observed and the content of BAs was within the acceptable limit throughout the fermentation of zaoyu. Significant differences in microbiota composition were observed between zaoyu and the controls. The bacterial community composition of zaoyu was relatively simple and Lactobacillus was identified as the dominant microbial group. The accumulation of histamine was inhibited in zaoyu, which was positively correlated with the relative abundance of Vibrio, Enterobacter, Macrococcus, Weissella, et al. based on Redundancy analysis (RDA), while Lactobacillus showed a positive correlation with tyramine, cadaverine, and putrescine. Functional predictions, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis, revealed that the relative abundance of metabolic function exhibited a decreasing trend with prolonged fermentation time and the abundance of metabolism-related genes was relatively stable in the later stage of fermentation. Those metabolisms related to the formation of BAs like histidine metabolism and arginine metabolism were inhibited in zaoyu. This study has accompanied microbiota analysis and functional metabolism with the accumulation of BAs to trace their correspondences, clarifying the roles of microorganisms in the inhibition of BAs during fermentation of Scomber japonicus.

Effects of sulfate concentration on anaerobic treatment of wastewater containing monoethanolamine using an up-flow anaerobic sludge blanket reactor

Monoethanolamine (MEA), a toxic organic chemical, is widely used in industries and is found in their wastewater. Anaerobic MEA degradation is an appropriate strategy to reduce energy and cost for treatment. Industry wastewaters also contain sulfate, but information on the effects of sulfate on MEA degradation is limited. Here, an up-flow anaerobic sludge blanket (UASB) for MEA-containing wastewater treatment was operated under psychrophilic conditions (18–20 ºC) to investigate the effects of sulfate on the microbial characteristics of the retained sludge. To acclimatize the sludge, the proportion of MEA in the influent (containing sucrose, acetate, and propionate) was increased from 15% to 100% of total COD (1500 mg L–1); sulfate was then added to the influent. The COD removal efficiency remained above 95% despite the increase in MEA and sulfate. However, granular sludge disintegration was observed when sulfate was increased from 20 to 330 mg L–1. Batch tests revealed that propionate and acetate were produced as the metabolites of MEA degradation. In response to sulfate acclimation, methane-producing activities for propionate and hydrogen declined, while sulfate-reducing activities for MEA, propionate, and hydrogen increased. Accordingly, acclimation and changes in dominant microbial groups promoted the acetogenic reaction of propionate by sulfate reduction.