Microbial Dynamics Research Articles

Effects of Phaffia rhodozyma on microbial community dynamics and tobacco quality during tobacco fermentation.

Carotenoids are important precursors of various aroma components in tobacco and play an important role in the sensory quality of tobacco. Phaffia rhodozyma is a species of Xanthophyllomyces capable of synthesizing a highly valuable carotenoid-astaxanthin, but has not yet been used in improving tobacco quality. The dynamic changes of microbial community and metabolites during tobacco fermentation were analyzed in combination with microbiome and metabolome, and the quality of tobacco after fermentation was evaluated by sensory scores. P. rhodozyma could grow and produce carotenoids in tobacco extract, with a maximum biomass of 6.50 g/L and a maximum carotenoid production of 36.13 mg/L at 100 g/L tobacco extract. Meanwhile, the correlation analysis combined with microbiome and metabolomics showed that P. rhodozyma was significantly positively correlated with 11 metabolites such as 6-hydroxyluteolin and quercetin. Furthermore, the contents of alcohols, ketones and esters, which were important aromatic components in fermented tobacco, reached 77.57 μg/g, 58.28 μg/g and 73.51 μg/g, increasing 37.39%, 265.39% and 266.27% compared to the control group, respectively. Therefore, the aroma and flavor, and taste scores of fermented tobacco increased by 0.5 and 1.0 points respectively. This study confirmed that P. rhodozyma fermentation could effectively improve the sensory evaluation of tobacco, and provided a novel microbial fermentation method to improve tobacco quality.

Polystyrene nanoparticles regulate microbial stress response and cold adaptation in mainstream anammox process at low temperature

Nanoplastic pollution has become one of the most pressing environmental issues, and its bioaccumulation in aquatic environment also causes a great difficulty in treatment. Therefore, this work investigated the microbial dynamics of mainstream anaerobic ammonia oxidizing (anammox) process to treat the wastewater containing typical nanoplastics, as well as the fate and regulation mechanism of polystyrene nanoparticles (PS-NPs) with different concentrations. The results showed that 0.1–0.5 mg L-1 of PS-NPs had no significant effect on the nitrogen removal efficiency (NRE). When the concentration of PS-NPs increased from 0.5 mg L-1 to 2 mg L-1, the NRE of R1 with PS-NPs decreased from 94.9 ± 2.3 % to 77.0 ± 1.6 %, while the control reactor R0 maintained a stable NRE. Notably, the relative abundance of Ca. Kuenenia decreased from 17.4 % to 14.8 %, and that of Ca. Brocadia slightly decreased from 5.9 % to 5.0 % in R1. In addition, PS-NPs induced oxidative stress in anammox consortia, leading to the significant increase in reactive oxygen species (ROS) and lactate dehydrogenase (LDH) as well as cell membrane damage. PS-NPs also downregulated the content of heme c and further inhibited anammox activity. Based on the molecular docking simulation and western blotting, cold shock proteins (CSPs) could bind to PS-NPs and reduce the performance of anammox processes at low temperatures.

Impacts of Polyvinyl Alcohol and Chitosan-Modified Biochar on the Anaerobic Digestion of Sewage Sludge and Valuable Resource Recovery

The accumulation of organic dyes and heavy metals (HMs) in sewage sludge (SS) after wastewater treatment is a significant problem due to the non-degradable nature of these pollutants. Moreover, the simultaneous removal of HMs and dyes in the complex process of SS treatment, such as anaerobic digestion (AD), has become attractive. HMs and dyes present in SS can have a detrimental effect on anaerobic digesters. These pollutants not only inhibit the production of methane, which is crucial for biogas generation, but also affect the stability of AD treatment, which can result in failure or inadequate performance of the AD process. This review highlights a novel method of removing HMs and dyes from the AD process of SS through the use of biochar modified with polyvinyl alcohol (PVA) and chitosan (CTS). The applications of conventional biochar have been limited due to poor adsorption capacity. However, modification using PVA/CTS composites enhances properties such as surface functional groups, adsorption capacity, porosity, surface area selectivity, and stability. Furthermore, this modified version can function as an additive in AD of SS treatment to boost biogas production, which is a viable source for heat generation or electricity supply. In addition, the digestates can be further processed through plasma pyrolysis for the removal of HMs and dyes bound to the modified biochar. Plasma pyrolysis generates two major products: syngas and slag. The syngas produced can then be used as a source of hydrogen, heat, and electricity, while the slag can potentially be reused as an AD additive or as a biofertilizer in the agricultural sector. Additionally, this study addresses the challenges associated with this integration and biochar modifications, and offers an outlook on understanding the interactions between the modified biochar properties, microbial dynamics, and the presence of micropollutants to ensure the economic viability and scalability of this technology. This comprehensive review provides insights into the potential of PVA/CTS-modified biochar as an effective additive in AD systems, offering a sustainable approach to SS treatment and valuable resource recovery.

Transient hypoxia drives soil microbial community dynamics and biogeochemistry during human decomposition.

Human decomposition in terrestrial ecosystems is a dynamic process creating localized hot spots of soil microbial activity. Longer-term (beyond a few months) impacts on decomposer microbial communities are poorly characterized and do not typically connect microbial communities to biogeochemistry, limiting our understanding of decomposer communities and their functions. We performed separate year-long human decomposition trials, one starting in spring, another in winter, integrating bacterial and fungal community structure and abundances with soil physicochemistry and biogeochemistry to identify key drivers of microbial community change. In both trials, soil acidification, elevated microbial respiration, and reduced soil oxygen concentrations occurred. Changes in soil oxygen concentrations were the primary driver of microbial succession and nitrogen transformation patterns, while fungal community diversity and abundance was related to soil pH. Relative abundance of facultative anaerobic taxa (Firmicutes and Saccharomycetes) increased during the period of reduced soil oxygen. The magnitude and timing of the decomposition responses were amplified during the spring trial relative to the winter, even when corrected for thermal inputs (accumulated degree days). Further, soil chemical parameters, microbial community structure, and fungal gene abundances remained altered at the end of 1 year, suggesting longer-term impacts on soil ecosystems beyond the initial pulse of decomposition products.

179 Charting the evolution of rumen microbial models from past to present

Abstract This review delves into the intricate realm of ruminal microbes, shedding light on their complexity beyond previously recognized dimensions. Existing publications have probed the essential facets of these microorganisms on a finer scale than previously acknowledged. Mathematical models have emerged to simulate the behavior of approximately 200 distinct bacterial species, 25 genera of ciliate protozoa, and five genera of anaerobic fungi, constituting about 10% of the total viable bacteria in the rumen. However, the expansive diversity and density of rumen microbes challenge the complete characterization of species or genera in relation to substrates or end products. Consequently, continuous revision and re-engineering of mathematical models become imperative. In the context of ruminants, prevalent models often categorize bacteria into fiber-fermenting and nonfiber-fermenting groups. An additional subgroup featuring hyper-ammonia-producing bacteria has been proposed, but its explicit integration into nutrition models remains unexplored. Furthermore, incorporating a more mechanistic evaluation of protozoa and fungal growth may be warranted to improve nutrition models. The time horizon and intervals at which models are constructed present another critical consideration, with feed efficiency variations among ruminants believed to be closely tied to differences in the ruminal microbiota. Addressing immediate concerns, this review underscores the need for a comprehensive exploration of factors influencing microbial growth in the rumen. Several indices have been suggested and adopted to predict microbial efficiencies, but they may provide simplification for practical application. Thus, a mechanistic approach should be considered to remove dependencies between estimates and improve predictive accuracy and precision. While artificial intelligence holds promise in elucidating gaps within empirical and mechanistic models, the generation of accurate, vetted datasets is paramount. Furthermore, this review posits that factors such as recycled nitrogen, endotoxins, and microbial population dynamics (i.e., cross-feeding and competition) may be limiting our understanding of microbial growth, suggesting the necessity of modeling these intricacies concurrently to achieve a more nuanced comprehension. This multifaceted approach aims to propel the understanding of ruminal microbial dynamics into new frontiers, paving the way for more informed and effective modeling in the future.

Microbial community dynamics in different floc size aggregates during nitrogen removal process upgrading in a full-scale landfill leachate treatment plant

Upgrading processes to reduce biodegradable organic substance addition is crucial for treating landfill leachate with high pollutant concentrations, aiding carbon emission reduction. Aggregate size in activated sludge processes impacts pollutant removal and sludge/water separation. This study investigated microbial community succession and driving mechanisms in different floc-size aggregates during nitrogen removal progress upgrade from conventional to partial nitrification–denitrification in a full-scale landfill leachate treatment plant (LLTP) using 16S rRNA gene sequencing. The upgrade and floc sizes significantly influenced microbial diversity and composition. After upgrading, ammonia-oxidizing bacteria were enriched while nitrite-oxidizing bacteria suppressed in small flocs with homogeneity and high mass transfer efficiency. Larger flocs enriched Defluviicoccus, Thauera, and Truepera, while smaller flocs enriched Nitrosomonas, suggesting their potential as biomarkers. Multi-network analyses revealed microbial interactions. A deep learning model with convolutional neural networks predicted nitrogen removal efficiency. These findings guide optimizing LLTP processes and understanding microbial community dynamics based on floc size.

Succession from acetoclastic to hydrogenotrophic microbial community during sewage sludge anaerobic digestion for bioenergy production.

To assess microbial dynamics during anaerobic digestion (AD) of sewage sludge (SWS) from a municipal Wastewater Treatment Plant (WWTP), a Biochemical Methane Potential (BMP) assay at 37°C under mono-digestion conditions was conducted. Utilizing the Illumina MiSeq platform, 16S ribosomal RNA (rRNA) gene sequencing unveiled a core bacterial community in the solid material, showcasing notable variations in profiles. The research investigates changes in microbial communities and metabolic pathways to understand their impact on the efficiency of the digestion process. Prior to AD, the relative abundance in SWS was as follows: Proteobacteria > Bacteroidota > Actinobacteriota. Post-AD, the relative abundance shifted to Firmicutes > Synergistota > Proteobacteria, with Sporanaerobacter and Clostridium emerging as dominant genera. Notably, the methanogenic community underwent a metabolic pathway shift from acetoclastic to hydrogenotrophic in the lab-scale reactors. At the genus level, Methanosaeta, Methanolinea, and Methanofastidiosum predominated initially, while post-AD, Methanobacterium, Methanosaeta, and Methanospirillum took precedence. This metabolic transition may be linked to the increased abundance of Firmicutes, particularly Clostridia, which harbor acetate-oxidizing bacteria facilitating the conversion of acetate to hydrogen.

Methanogenic degradation of long-chain fatty acids associated with syntrophic microbial dynamics during thermophilic AnMBR treatment of lipid-rich dairy wastes

Anaerobic membrane reactors (AnMBRs) have been applied to effectively treat dairy wastes because they can address the drawbacks of sludge flotation and biomass washout. However, when dairy wastes contain considerable proportion of lipids, any anaerobic systems will likely encounter challenges with long-chain fatty acid (LCFA) inhibition. In this study, a thermophilic AnMBR was operated to treat dairy processing wastewater (DPW) plus ice cream waste (ICW). To evaluate the impact of LCFAs, the lipid-rich ICW was gradually introduced at different levels (0, 5, 10, and 20 %) into the AnMBR, along with a stepwise increase in lipid loading rate (LLR) from 0.22 to 11.24 g lipid/L/d. The results of biomethanation revealed that the AnMBR could be successfully operated when the LLR was maintained at 5.73 g lipid/L/d with a lipid/VS ratio of 50.22 % in the feedstock. However, at ultra-high LLR of 11.24 g lipid/L/d (20 % ICW added), a significant inhibitory effect on methane yields was observed, resulting in a reduction of 56.90 %. Dynamic analysis of the LCFAs profiled that a lower degradation rate was an important factor contributing to LCFA accumulation, and the inhibition concentration of various LCFAs was identified. Based on microbial evolution and co-occurrence network results, potential syntrophic partnerships between LCFA-degrading bacteria and methanogens were proposed. The responsible enzyme genes in the LCFA-degrading, acetoclastic, and hydrogenotrophic methanogenic pathways played crucial roles in LCFA inhibition and degradation. These findings offer practical insights for the efficient methanogenic treatment of lipid-rich wastes.

Brining as an effective method to stabilise sea lettuce (Ulva fenestrata) -impact on colour, texture, chemical characteristics and microbial dynamics

Brining as a cost-effective stabilising method to preserve the quality of fresh Ulva fenestrata was studied. The brines contained from 0 to 25 % (w/w) of sodium chloride or from 0 to 50 % sucrose and were combined with seaweed at a ratio of 1: 10 (w/v) prior to storage at 4 °C for up to 3 months. During this storage, the water activity of U. fenestrata was reduced from 0.94 to ≤0.89 with ≥15 % salt brines, which kept the microbial load <7 log (CFU/g) for 78 days. Among the sucrose brines, 50 % provided microbial shelf life <7 log (CFU/g) for 48 days. Further, 25 % salt or 50 % sucrose brines effectively retained the greenness (a*) of the U. fenestrata blades (< −20 a*-value for 80 days), while the tensile strength was only retained with 25 % salt brine (>3 Newton for 80 days). There was a time-dependent loss of crude proteins and fatty acids during storage, especially for 50 % sugar brined seaweed, where 58 % and 28 %, respectively, were lost after 20 days. Nutrients were best preserved in the 5 % salt-brine. Overall, the results indicate that brining with 25 % salt or 50 % sugar yields microbial stability and maintained colour of U. fenestrata for at least 48 days, with the former even exceeding 78 days at 4 °C, however, at a cost of nutritional value.

Management of Spartina alterniflora: Assessing the Efficacy of Plant Growth Regulators on Ecological and Microbial Dynamics

Spartina alterniflora is recognized as one of the most detrimental invasive species along China’s coastlines, highlighting the need for effective and environmentally safe management strategies to preserve intertidal zones. This study assessed the effectiveness of combining plant growth regulators (PRGs) with physical cutting to manage S. alterniflora, using 16S rRNA and 18S rRNA gene sequencing to evaluate the impacts on the plant and associated soil micro-organisms. The results showed that compared to the control (CK), the regeneration numbers for treatments with abscisic acid (ABA), gibberellin (GA), paclobutrazol (PP333), garcinol (GC), and glyphosate (GP) decreased by 29.75%, 23.25%, 15.75%, 94.50%, and 40.50%, respectively. Comparative analysis revealed no statistically significant variation in the inhibitory effects of ABA and GP on the germination of S. alterniflora (p &gt; 0.05). Additionally, applying PRGs and herbicides increased the diversity indices of soil bacteria and fungi. Principal Coordinates Analysis (PCoA) showed that the impact of PRGs on the fungal community was less pronounced than that of herbicides. Significant differences were also noted in the abundance of microbial functional genes related to methanotrophy, hydrocarbon degradation, and denitrification compared to the control (p &lt; 0.05). This study aimed to assess the potential of PRGs in controlling the invasion of S. alterniflora and to elucidate their impacts on soil microbial communities and functional gene expression.

Microbial dynamics, chemical profile, and bioactive potential of diverse Egyptian marine environments from archaeological wood to soda lake

Halophilic archaea are a unique group of microorganisms that thrive in high–salt environments, exhibiting remarkable adaptations to survive extreme conditions. Archaeological wood and El–Hamra Lake serve as a substrate for a diverse range of microorganisms, including archaea, although the exact role of archaea in archaeological wood biodeterioration remains unclear. The morphological and chemical characterizations of archaeological wood were evaluated using FTIR, SEM, and EDX. The degradation of polysaccharides was identified in Fourier transform infrared analysis (FTIR). The degradation of wood was observed through scanning electron microscopy (SEM). The energy dispersive X–ray spectroscopy (EDX) revealed the inclusion of minerals, such as calcium, silicon, iron, and sulfur, into archaeological wood structure during burial and subsequent interaction with the surrounding environment. Archaea may also be associated with detected silica in archaeological wood since several organosilicon compounds have been found in the crude extracts of archaeal cells. Archaeal species were isolated from water and sediment samples from various sites in El–Hamra Lake and identified as Natronococcus sp. strain WNHS2, Natrialba hulunbeirensisstrain WNHS14, Natrialba chahannaoensis strain WNHS9, and Natronococcus occultus strain WNHS5. Additionally, three archaeal isolates were obtained from archaeological wood samples and identified as Natrialba chahannaoensisstrain W15, Natrialba chahannaoensisstrain W22, and Natrialba chahannaoensisstrain W24. These archaeal isolates exhibited haloalkaliphilic characteristics since they could thrive in environments with high salinity and alkalinity. Crude extracts of archaeal cells were analyzed for the organic compounds using gas chromatography–mass spectrometry (GC–MS). A total of 59 compounds were identified, including free saturated and unsaturated fatty acids, saturated fatty acid esters, ethyl and methyl esters of unsaturated fatty acids, glycerides, phthalic acid esters, organosiloxane, terpene, alkane, alcohol, ketone, aldehyde, ester, ether, and aromatic compounds. Several organic compounds exhibited promising biological activities. FTIR spectroscopy revealed the presence of various functional groups, such as hydroxyl, carboxylate, siloxane, trimethylsilyl, and long acyl chains in the archaeal extracts. Furthermore, the archaeal extracts exhibited antioxidant effects. This study demonstrates the potential of archaeal extracts as a valuable source of bioactive compounds with pharmaceutical and biomedical applications.

Soil Microbial Properties of Durum Grown after Camelina, Carinata, Cover Crops, and Fallow

Novel crop rotation is an important factor influencing the composition of soil microorganisms. However, the effect of introducing oilseed and cover crops (CCs) into monoculture durum rotations on soil microbial communities is not clear in the Northern Great Plains. The objective of this study was to evaluate the effects of 2-year durum (Triticum durum D.) rotations with Ethiopian mustard (Brassica carinata A.) or camelina (Camelina sativa L.) or a 10-species forage/CC mix planted to replace fallow rotations with wheat on soil microorganisms. This study was designed as a randomized complete block with three replications in a no-tillage system. The results showed that total bacterial proportion was significantly higher in durum following fallow and camelina compared to durum following CC and carinata. Total fungal proportion was significantly higher in durum following CC compared to durum following oilseed crops and fallow. The fungal-to-bacterial ratio was significantly higher in durum following CC compared to durum following camelina and fallow. The crop species, soil pH and highly variable rainfall influenced the microbial community dynamics. The abundance of specific microbial groups due to crop-related changes might play a key role in the yield of subsequent crops and soil biological health. This study provides valuable insights into the use of CC mix and oilseeds as an alternative crop for fallow in a wheat–fallow system under dryland farming conditions. Future work is required to elucidate the biological mechanisms and functions of the soil microbial communities in the preceding and subsequent crop relative to soil health and crop productivity.

Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications.

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.

The Addition of Glutamine Enhances the Quality of Huangjiu by Modifying the Assembly and Metabolic Activities of Microorganisms during the Fermentation Process.

In this study, the effects of adding glutamate (Glu), glutamine (Gln), aspartate (Asp), and asparagine (Asn) on the flavor formation of Huangjiu were investigated, and the effect of Gln concentration on the quality, microbial community structure, and flavor development of Huangjiu was further explored. Varied Gln concentrations influenced yeast growth, sugar utilization, microbial communities, and quality attributes. Additional Gln promoted yeast cell counts and sugar depletion. It increased the complexity of bacterial co-occurrence networks and reduced the impact of stochastic processes on assembly. Correlation analysis linked microorganisms to flavor compounds. Isolation experiments verified the role of Saccharomyces cerevisiae, Aspergillus chevalieri, Bacillus altitudinis, and Lactobacillus coryniformis in flavor production under Gln conditions. This research elucidated the microbiological mechanisms by which amino acid supplementation, especially Gln, enhances Huangjiu quality by modulating microbial metabolic functions and community dynamics during fermentation. This research is significant for guiding the production of Huangjiu and enhancing its quality.

Exploring naphthalene vapor biofiltration: performance and microbial community dynamics with diverse inoculums

AbstractBackgroundNaphthalene is a polycyclic aromatic hydrocarbon, highly dangerous for human health. It is produced as a byproduct of incomplete combustion of organic material and is frequently present in the air. Biofilters offer an effective alternative for its treatment. The aim of this work was to study the treatment of naphthalene vapors through biofiltration using two biofilters: one inoculated with a consortium composed of Fusarium solani and Rhodococcus erythropolis (BF1), and the other inoculated with a consortium of microbial isolates obtained from a previous biofilter eliminating naphthalene vapors.ResultsThe results demonstrate that inoculating a biofilter with a reconstructed consortium of microbial isolates from a naphthalene vapor‐eliminating biofilter allowed a reduction of the startup time from 35 to 5 days, while maintaining a consistent removal capacity (6 g m−3 h−1, equivalent to 80% removal efficiency). It was also observed that the biofilter inoculated with the reconstructed consortium exhibited comparable robustness to a biofilter previously operated for 4 months with naphthalene, with a maximum removal capacity of 14 g m−3 h−1 for a naphthalene inlet load of 17 g m−3 h−1. The study of microbial communities indicates an increase in the bacterial variability, while fungal variability remains low, with Fusarium solani being predominant at 97%.ConclusionsResults obtained during the startup of both biofilters and by challenging biofilters to increasing naphthalene concentrations or decreasing empty bed residence time showed that startup time can be reduced sevenfold by selecting the microbial consortium. An equivalent performance, in the long run, was achieved for both biofilters. © 2024 Society of Chemical Industry (SCI).

Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea

This comprehensive two-year investigation in the coastal South China Sea has advanced our understanding of marine microbes at both community and genomic levels. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. We observed distinct seasonal shifts in microbial community composition and function: cyanobacteria were predominant during warmer months, whereas photosynthetic protists were more abundant during colder seasons. Notably, metabolic marker KOs of photosynthesis were consistently active throughout the year, underscoring the persistent role of these processes irrespective of seasonal changes. Our analysis reveals that environmental parameters such as temperature, salinity, and nitrate concentrations profoundly influence microbial community composition, while temperature and silicate have emerged as crucial factors shaping their functional traits. Through the recovery and analysis of 37 phytoplankton MAGs, encompassing nine prokaryotic cyanobacteria and 28 eukaryotic protists from diverse phyla, we have gained insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways including carbon fixation, carotenoid biosynthesis, photosynthesis-antenna proteins, and photosynthesis among the MAGs indicated their genetic adaptations to changing environmental conditions. This study not only enhances our understanding of microbial dynamics in coastal marine ecosystems but also sheds light on the ecological roles and adaptive responses of different microbial groups to environmental changes.

Investigation on the Distribution of Antibiotic Resistant Bacteria In Dry Fish of Chalan Beel Area From Northwestern Part of Bangladesh

Dried fish, a valuable animal protein source, may pose health risks due to microbial contamination influenced by water quality, hygiene practices, handling, packaging, and transportation. This research focuses on conducting an in-depth analysis of the occurrence and antibiotic resistance patterns of bacteria, identified through 16S rRNA sequencing, in different dried fish varieties obtained from the Chalan beel area in Northwestern Bangladesh. For the purpose of this study, homogenization of collected samples was carried out and resulting homogenates were refrigerated at a temperature of -20°C. Then the samples were subjected to a series of 10-fold dilutions and spread over 1.5% nutrient agar supplemented with Tetracycline. Thereafter, plates were incubated at 37°C for a duration of 24 hours to form bacterial colonies. Twelve aseptically collected dried fish samples had a total viable count ranging from 2.0 × 10² to 6.5 × 10⁵ CFU/ml, with tetracycline influence at 32 µg/ml (7 × 10² to 5.4 × 10³ CFU/ml) and 64 µg/ml (3.0 × 10² to 2.1 × 10³ CFU/ml). Notably, Tengra fish (Mystus sp.) exhibited the highest viable count 6.5 × 105 CFU/ml (Control), while Darikana (Esomus danricus), Chela (Salmostoma phulo), Moa (Amblypharyngodon mola), and Guchi (Mastacembelus pancalus) fish showed the lowest count (3.0 × 10² CFU/ml) at a Tetracycline concentration of 64 µg/ml. Moreover, microbial analysis using 16S rRNA gene sequencing identified twelve unique bacteria belong to genera. The most prevalent genus appears to be Enterobacter, identified by 6 strains. These include Enterobacter hormaechei strains UCHE20, RB13, AUH-ENM30 and 20710, Enterobacter ludwigii strain JCR-38 and Enterobacter sp. M3. Other identified genera included Klebsiella (with Klebsiella variicola and Klebsiella pneumoniae), Proteus (Proteus mirabilis), Macrococcus (Macrococcus caseolyticus), Acinetobacter (Acinetobacter johnsonii), and Bacillus (Bacillus sp.). This study provides valuable insights into the complex microbial dynamics in dried fish, emphasizing the need for enhanced food safety and public health measures. J. Bio-Sci. 32(2): 61-69, 2024

Isotope analysis of nitrogen removal pathways and N2O production potential in the SDAD-anammox system under different N/S ratios

This study explored the impact of varying nitrate to sulfide (N/S) ratios on nitrogen removal efficiency (NRE) in the sulfide-driven autotrophic denitrification and anammox (SDAD-anammox) system. Optimal nitrogen removal was observed at N/S ratios between 1.5 and 2.0. Isotope tracing results showed that the contribution of anammox to nitrogen removal was enhanced with increasing N/S ratios, reaching up to 37 % at the N/S ratio of 2.5. Additionally, complex nitrogen pathways were identified, including dissimilatory nitrate reduction to ammonium (DNRA). Furthermore, isotope tracing was innovatively applied to investigate N2O emissions, demonstrating that higher N/S ratios significantly reduced N2O emissions, with the lowest emissions at N/S ratio of 2.5. Gene expression analysis indicated that nitrogen and sulfide transformation genes decreased with increasing N/S ratios, while anammox-related genes first increased and then decreased, reflecting the system's microbial dynamics. These findings offer insights into nitrogen transformation pathways and N2O production mechanisms in the SDAD-anammox process.

Combined inorganic and organic fertilizers improved soil microbial biomass and nitrogen dynamics in Upper Eastern region of Kenya

Soil microbial biomass elements and mineralization processes are essential in replenishing soil nutrients. Yet, the effect of fertilization on the microbes is still not well-defined. This study aimed to determine the effect of integrated soil fertility inputs (inorganic and organic) on microbial biomass, carbon (MBC), nitrogen (MBN), phosphorus (MBP), nitrogen (N) mineralization, and N use efficiency in a field experiment. The treatments were: control (no fertility input), sole inorganic fertilizer, and different combinations of inorganic and organic inputs in a randomized block design. The results showed that Conventional tillage + maize residue + goat manure + Dolichos lablab intercrop (CT4); minimum tillage + maize residue + Tithonia diversifolia + goat manure (MT5); and minimum tillage + maize residue + goat manure + Dolichos lablab (MT4) intercrop increased microbial C, N, and P by 78 %, 48 %, and 41 %, respectively compared to control (CT0). Compared to CT0, N mineralization significantly varied (p < 0.0001) among the treatments at planting and on the 15th, 30th, 45th, and 60th days after planting during the 2020 short rains season. It also differed significantly (p = 0.0018, 0.0028, < 0.0001, and 0.0028,) on the 45th, 60th, 75th, 90th, and 105th days, respectively, relative to CT0 after planting during the 2021 long rains season. The CT4 had 5.11 and 52.80 kg N ha−1 higher apparent nitrogen recovery and partial factor productivity N, respectively. Similarly, MT4 greatly enhanced N apparent recovery efficiency by 57.5 % relative to CT0. Integrating fertility inputs improved soil biological fertility and mineralized N. Therefore, technologies that integrate organic inputs, either solely or with inorganic fertilizers, should be harnessed and promoted as medium and long-term technologies to advance soil biological fertility, and mineral N and N use efficiency in smallholder farmers.

Microbiomics and metabolomics insights into the microbial regulation on the formation of flavor components in the traditional fermentation process of Chinese Hongqu aged vinegar

This study aimed to investigate microbial succession and metabolic dynamics during the traditional fermentation of Hongqu aged vinegar, and explore the core functional microbes closely related to the formation of flavor components. Microbiome analysis demonstrated that Lactobacillus, Acetobacter, Bacillus, Enterobacter, Lactococcus, Leuconostoc and Weissella were the predominant bacterial genera, while Aspergillus piperis, Aspergillus oryzae, Monascus purpureus, Candida athensensis, C. xylopsoci, Penicillium ochrosalmoneum and Simplicillium aogashimaense were the predominant fungal species. Correlation analysis revealed that Acetobacter was positively correlated with the production of tetramethylpyrazine, acetoin and acetic acid, Lactococcus showed positive correlation with the production of 2-nonanone, 2-heptanone, ethyl caprylate, ethyl caprate, 1-hexanol, 1-octanol and 1-octen-3-ol, C. xylopsoci and C. rugosa were positively associated with the production of diethyl malonate, 2,3-butanediyl diacetate, acetoin, benzaldehyde and tetramethylpyrazine. Correspondingly, non-volatile metabolites were also detected through ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. A variety of amino acids and functional dipeptides were identified during the traditional brewing of Hongqu aged vinegar. Correlation analysis revealed that Lactobacillus was significantly associated with DL-lactate, indolelactic acid, D-(+)-3-phenyllactic acid, pimelic acid, pregabalin and 3-aminobutanoic acid. This study is useful for understanding flavor formation mechanism and developing effective strategies for the suitable strains selection to improve the flavor quality of Hongqu aged vinegar.