Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction

Outbreaks of Ulva prolifera green tides reduce the network complexity and stability of cooccurring planktonic microbial communities

Ulva prolifera green tides are becoming a worldwide environmental problem, especially in the Yellow Sea, China. However, the effects of the occurrence of U. prolifera green tides on the community organization and stability of surrounding microbiomes have still not been determined. Here, the prokaryotic microbial community network stability and assembly characteristics were systematically analyzed and compared between the green tide and non-green tide periods. U. prolifera blooms weaken the community complexity and robustness of surrounding microbiomes, increasing fragmentation and decreasing diversity. Bacteria and archaea exhibited distinct community distributions and assembly patterns under the influence of green tides, and bacterial communities were more sensitive to outbreaks of green tides. The bacterial communities exhibited a greater niche breadth and a lower phylogenetic distance during the occurrence of U. prolifera green tides compared to those during the non-green tide period while archaeal communities remained unchanged, suggesting that the bacterial communities underwent stronger homogeneous selection and more sensitive to green tide blooms than the archaeal communities. Piecewise structural equation model analysis revealed that the different responses of major prokaryotic microbial groups, such as Cyanobacteria, to environmental variables during green tides, were influenced by the variations in pH and nitrate during green tides and correlated with the salinity gradient during the non-green tide period. This study elucidates the response of the adaptability, associations, and stability of surrounding microbiomes to outbreaks of U. prolifera green tides.

Shift in activated sludge microbiomes associated with nitrite accumulation and high nitrous oxide emissions

Nitrous oxide (N2O) emissions can constitute over half of the carbon footprint of a wastewater treatment plant (WWTP), and emission peaks frequently correlate with nitrite (NO2-) concentrations. However, connections between the microbiome and high N2O and NO2- levels are not well-documented. Here, we characterize the microbiomes in several parallel lines of a WWTP during massive N2O emissions (20 % of influent nitrogen load) with prolonged NO2- accumulation in most lines, aiming to identify key differences between communities in lines with high and low NO2- concentrations. The abundance of nitrite-oxidizing bacteria (NOB) was extremely low in the lines with NO2- accumulation, which also had slightly lower abundances of ammonia-oxidizing bacteria (AOB). Some incomplete denitrifiers were more abundant in the lines with NO2- accumulation. Lines without NO2- had a higher relative abundance of filamentous bacteria and better floc formation. These findings confirmed our hypothesis that loss of NOB caused NO2- accumulation, inducing increased N2O emissions. AOB are suspected to be the main source of N2O during the studied period, with a likely contribution from heterotrophic denitrifiers. A few species were identified as interesting candidates for further study regarding their potential role in increased N2O emission from WWTPs. Long-term microbiome monitoring is necessary to understand the changes in the microbiome that might initiate NO2- accumulation and high N2O emissions.

Nannochloropsis oceanica IMET1 and its bacterial symbionts for carbon capture, utilization, and storage: biomass and calcium carbonate production under high pH and high alkalinity

To combat the increasing levels of carbon dioxide (CO2) released from the combustion of fossil fuels, microalgae have emerged as a promising strategy for biological carbon capture, utilization, and storage. This study used a marine microalgal strain, Nannochloropsis oceanica IMET1, which thrives in high CO2 concentrations. A high-pH, high-alkalinity culture was designed for CO2 capture through algal biomass production as well as permanent sequestration through calcium carbonate (CaCO3) precipitation. This was accomplished by timed pH elevation and the addition of sodium bicarbonate to cultures of N. oceanica grown at lab scale (1 L) and pilot scale (500 L) with 10% and 5% CO2, respectively. Our data showed that 0.02 M NaHCO3 promoted algal growth and that sparging cultures with ambient air after 12 days raised pH and created favorable CaCO3 formation conditions. At the 1 L scale, we reached 1.52 g L-1 biomass after 12 days and an extra 9.3% CO2 was captured in the form of CaCO3 precipitates. At the 500 L pilot scale, an extra 60% CO2 was captured (Day 40) with a maximum CO2 capture rate of 63.2 g m-2 day-1 (Day 35). Bacterial communities associated with the microalgae were dominated by two novel Patescibacteria. Functional analysis revealed that genes for several plant growth-promotion traits (PGPTs) were enriched within this group. The microalgal-bacterial coculture system offers advantages for enhanced carbon mitigation through biomass production and simultaneous precipitation of recalcitrant CaCO3 for long-term CO2 storage.IMPORTANCECapturing carbon dioxide (CO2) released from fossil fuel combustion is of the utmost importance as the impacts of climate change continue to worsen. Microalgae can remove CO2 through their natural photosynthetic pathways and are additionally able to convert CO2 into a stable, recalcitrant form as calcium carbonate (CaCO3). We demonstrate that microalgae-based carbon capture systems can be greatly improved with high pH and high alkalinity by providing optimal conditions for carbonate precipitation. Our results with the microalga, Nannochloropsis oceanica strain IMET1, show an extra 9.3% CO2 captured as CaCO3 at the 1 L scale and an extra 60% CO2 captured at the 500 L (pilot) scale. Our optimized system provides a novel approach to capture CO2 through two mechanisms: (i) as organic carbon within microalgal biomass and (ii) as inorganic carbon stored permanently in the form of CaCO3.

Microbial acclimation of thermophilic anaerobic digestate enhances biogas production and biodegradation of polylactic acid in combination with the organic fraction of municipal solid waste (OFMSW)

Bioplastics are a promising alternative to conventional plastics. Their anaerobic co-digestion with the organic fractions of municipal solid waste (OFMSW) is an ideal end-of-life scenario reducing pre-treatment and increasing efficiency and biogas production. Bioplastic degradation is limited under anaerobic digestion (AD) as it requires longer hydraulic retention time (HRT) compared to industrial OFMSW plants' HRTs. Here, three AD runs were conducted sequentially under thermophilic conditions to investigate the effects of inoculum acclimation on enhancing the degradation of polylactic acid (PLA) and OFMSW in mono and co-digestion (PLA + OFMSW). In PLA mono-digestion, microbial acclimation increased biogas production up to +152 % (831 ± 11 NL kgVS-1) and biogas production rate from 27 to 47 NL kgVS-1 d-1 with a 5-day reduction of the lag phase. This improvement was associated with the enrichment of the PLA-degrading bacteria Tepidanaerobacter. In PLA + OFMSW co-digestion, biogas production increased of +69 % (827 ± 69 NL kgVS-1), the biogas production rate increased to 58 NL kgVS-1 d-1 with a lag phase reduction of 7 days. An increase of both protein degraders (Halocella and Acetomicrobium) and Tepidanaerobacter was achieved. In OFMSW mono-digestion, acclimation increased cumulative biogas production to + 22 % (719 ± 25 NL kgVS-1) with no biogas production rate and lag phase modifications, indicating an already adapted community. A variance in Methanothermobacter and Metanoculleus abundances across treatments was linked to different biomethane productions. Microbial acclimation is a valid and economical approach to enhance biogas production and PLA degradability, alone or with OFMSW, further reducing HRTs enabling sustainable bioplastic and OFMSW waste management.

Encapsulated phytogenic oils enhance in vitro rumen fermentation and reduce methane emissions

BACKGROUND

This research aimed to investigate bioaccessibility of garlic oil extract (GOE) and riceberry rice bran oil extract (RBRBOE) and to enhance the stability and delivery of plant-derived essential oils. Two EOs were used to formulate through encapsulation techniques of microencapsulated black soldier fly (BSF) protein with a GOE matrix, (mBSF-GOE), and a nanoemulsified RBRBOE, (nRBRBOE). A completely randomized design was used for the treatments, with various ratios of feed additives between the mBSF-GOE and nRBRBOE supplementations at 0:0, 6:0, 4:2, 2:4, and 0:6 mg in diet, with the R: C ratio at 60:40 using in vitro gas study.

RESULTS

The combination of mBSF-GOE and nRBRBOE at 4:2 mg for 12 and 24 h after fermentation had a significant impact on several factors (p < 0.01, < 0.05), including gas kinetics, cumulative gas production (96 h), in vitro dry matter degradability (IVDMD), and ruminal fermentation products. Specifically, the levels of propionate (C3) and total VFAs went up, while ruminal methane (CH4) production decreased by 48.2%. Subsequently, there was no negative effect (p > 0.05) on the ruminal pH, ammonia nitrogen (NH3-N) concentration, or the dynamics of the rumen microbiota population, while significantly decreasing the methanogen population in terms of Methanobacteriales (up to 3.3% after 24 h) (p < 0.01).

CONCLUSIONS

Based on this study, it could be concluded that the supplementation of mBSF-GOE combined with nRBRBOE-based bioactive components could potentially be used as a ruminant feed enhancer to enhance fermentation efficiency and as technological feed additive substances to inhibit the methanogen population while mitigating CH4 production.

Nanoemulsified Corn Oil in Lactating Barki Nutrition: Effect on Intake, Nutrient Digestibility, Rumen Fermentation Characteristics, and Microbial Population

Nanoemulsified corn oil was tested on twenty-one multiparous lactating Barki ewes (mean ± SD: 3 ± 0.4 parity, 44.3 ± 1.9 kg body weight, 30 ± 2.7 months of age, and 402 ± 23 g/d of prior milk production) randomly allocated to the following treatments (n = 7 ewes/group): Control-a basal diet consisting of 50% concentrate mixtures and 50% berseem clover; CO-the Control diet + 3% of corn oil; NCO-the Control diet + 3% of nanoemulsified corn oil. A completely randomized design of 25 days of adaptation and 5 days of sampling was employed with seven ewes per treatment. Despite feeding oil according to the recommended values, CO decreased the dry matter intake by 8.3% and 6.7% compared to the Control and NCO, respectively. The negative impact of CO extended to reducing the concentrations of ammonia and total volatile fatty acids in the rumen. On the other hand, NCO had less effect on the biohydrogenation intermediates profile compared to CO; noticeably, higher proportions of unsaturated fatty acid (UFA) were associated with NCO; these results were also supported by an increase in the rumen microbial population with NCO compared to CO, especially the biohydrogenation bacteria, which showed higher abundance with NCO despite the low presence of biohydrogenation intermediates. In conclusion, the NCO demonstrated the ability to decrease the transformation of unsaturated fatty acids into saturated fatty acids in the biohydrogenation environment. This effect was not associated with decreased dry matter intake, changes in nutrient digestibility, or alterations in fermentation patterns.

Physicochemical properties of carbon-based materials enhance in situ biomethanation performances under organic overload

Carbon-based materials gained attention for their potential to improve anaerobic digestion (AD) performance. Meanwhile, in situ biomethanation, where external H2 is injected into the AD process to enhance the CH4 content in biogas, is more subjected to process inhibition than AD while facing sudden changes in operational parameters. This study explored the effects of carbon-based materials on a semi-continuous in situ biomethanation process performance and stability. Two biochars and one granular activated carbon were tested at a concentration of 10 g·L-1. The experiment was conducted in three phases: a one-week start-up phase in AD conditions, an 8-week phase of in situ biomethanation, reaching a steady state, and a 2-week overload phase performed to create instability during the in situ biomethanation process. All additives significantly mitigated process failure under overload conditions, with CH4 production reaching 117 ± 16 vs 160 ± 16 NmL CH4·d-1 on the first week of organic overload (control vs average of all supplemented conditions). Specifically, the use of GAC-BC, with the highest surface area, pore volume, and diameter, led to a tenfold increase in CH4 production compared to the control in the overload phase. This improvement was associated with higher archaeal diversity and dominance of the Bacteroidales class. Conversely, the biochars, with lower surface properties, did not enhance microbial growth or improve final VFA consumption, resulting in final VFA concentrations similar to the control (11gCOD·L-1). These findings highlight the importance of surface properties in additives for mitigating VFA accumulation under stressed conditions during in situ biomethanation.

Impact of Blastocystis carriage and colonization intensity on gut microbiota composition in a non-westernized rural population from Colombia

BACKGROUND

The role of Blastocystis, a common intestinal parasitic protist of humans and other animals, in human health and disease remains elusive. Recent studies suggest a connection between Blastocystis colonization, healthier lifestyles, and high-diversity gut microbiota. Nevertheless, studies concerning the relationship between Blastocystis colonization, its intensity, and gut microbiota composition -involving both bacterial and eukaryotic communities- remain limited.

METHODS

This study examines the impact of Blastocystis carriage and colonization intensity on gut microbiota composition in a rural community in Colombia. A total of 88 human samples were collected from the rural population of Las Guacas village, located in the Cauca department in southwest Colombia. We utilized 16S and 18S rDNA sequencing to analyze both bacterial and eukaryotic microbiota, comparing Blastocystis-positive and -negative individuals, as well as groups with varying Blastocystis colonization intensity (low, medium, high), to identify distinct microbiota profiles and differentially abundant taxa linked to each condition.

RESULTS

The analysis revealed significant differences between Blastocystis-positive and -negative individuals. In terms of bacterial composition and structure, Blastocystis-positive individuals exhibited distinct microbiota profiles, as shown by beta diversity analysis. Taxa associated with colonization included Bacteroides, Prevotella, Oscillibacter, Faecalibacterium, and Alistipes. Higher Blastocystis colonization intensity was associated with an increased abundance of taxa such as Alistipes and Lachnospira, while lower intensities correlated with beneficial bacteria such as Akkermansia. Regarding eukaryotic composition, beta diversity analysis revealed distinct profiles associated with Blastocystis colonization. Differentially abundant taxa, including Entamoeba coli, were more prevalent in Blastocystis-positive individuals, while Blastocystis-negative individuals exhibited a higher abundance of opportunistic fungi, such as Candida albicans. Machine learning models, including random forest classifiers, supported these findings, identifying Faecalibacterium and Bacteroides as predictors of Blastocystis colonization.

CONCLUSIONS

These findings suggest that Blastocystis may modulate gut microbiota, contributing to microbial balance providing new insights into the ecological implications of Blastocystis in rural populations.

Tribenuron-methyl inhibited greenhouse gas emission and impacted the related functional pathways

This study investigates the combined effects of tribenuron-methyl and urea on soil bacterial communities, greenhouse gases emissions, and carbon (C) and nitrogen (N) cycle-related functions. High-throughput sequencing revealed significant impacts on bacterial diversity and composition, with responses varying across different concentrations, sampling times, and the presence of urea. Tribenuron-methyl inhibited bacterial diversity at early sampling times but increased diversity after 60 days in the highest treatment. The impact on bacterial phyla varied across treatments, with notable fluctuations in Proteobacteria, Chloroflexi, and Verrucomicrobiota abundance. Tribenuron-methyl also caused distinct shifts in bacterial community structure, with pronounced effects in the presence of urea. Tribenuron-methyl significantly suppressed CO2 release but had no significant effect on N2O emissions. Urea addition enhanced N2O release without altering the impact of tribenuron-methyl. Functional pathway analysis indicated that tribenuron-methyl inhibited C cycle-related enzymes, particularly without urea addition, while its effect on N cycle-related enzymes was minimal. These findings highlight the dynamic interactions between herbicides, nitrogen fertilizers, and soil microbial processes, offering insights into their ecological impacts and implications for agricultural management.

Do digestates produced by co-digestion of biowaste and biodegradable plastic affect soil and aquatic organisms?

The fast development of the biogas sector requires a better understanding of potential ecotoxicological effects of digestates on both terrestrial (through digestate spreading) and aquatic organisms (through digestate soil leachate). This study is the first one to assess through a multi-species approach that include aquatic organisms short-term ecotoxicological effect in microcosm experiments of digestates (and their respective leachates) derived from biowastes co-digested or not with biodegradable plastics (PLA or PHB). Ecotoxicological tests were performed on six terrestrial/aquatic bioindicators: (1) wheat, (2) tomato, (3) soil bacteria, (4) earthworm, (5) duckweed and (6) water flea. Digestate fertilization treatments were compared to a soil not fertilized and to a mineral fertilization ensuring the same level of N (170 kg N/ha) and P (17 kg P/ha) for all fertilized treatments. No ecotoxicities of all digestates and their soil leachates were observed on wheat, soil bacteria, earthworm, duckweed and water flea following laboratory standardized procedures. Attention should be given to possible ecotoxicity of biowaste digestates (with or without biodegradable plastics) on tomato growth where a lower dry aerial biomass (23 % less in average) was observed compared to the soil chemically fertilized. For all bioindicators, no differences were observed when comparing fertilization with biowaste digestate to its equivalent co-digested with biodegradable plastics. Therefore, no apparent ecotoxicity related to the potential presence of residual biodegradable plastics in digestates was highlighted. Long-term ecotoxicological effects and repeated exposure to biodegradable plastics from digestates as well as comparison with conventional plastics are beyond the scope of this article and will require further research.

Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State

Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.

Disruption-induced changes in syntrophic propionate and acetate oxidation: flocculation, cell proximity, and microbial activity

BACKGROUND

Syntrophic propionate- and acetate-oxidising bacteria (SPOB and SAOB) play a crucial role in biogas production, particularly under high ammonia conditions that are common in anaerobic degradation of protein-rich waste streams. These bacteria rely on close interactions with hydrogenotrophic methanogens to facilitate interspecies electron transfer and maintain thermodynamic feasibility. However, the impact of mixing-induced disruption of these essential syntrophic interactions in biogas systems remains largely unexplored. This study investigates how magnetic stirring and orbital shaking influence degradation dynamics, microbial community composition, and gene expression in syntrophic enrichment communities under high-ammonia conditions.

RESULTS

Stirring significantly delayed the initiation of propionate degradation in one culture and completely inhibited it in the other two parallel cultures, whereas acetate degradation was less affected. Computational fluid dynamics modelling revealed that stirring generated higher shear rates (~ 20 s-1) and uniform cell distribution, while shaking led to lower shear rates and cell accumulation at the bottom of the culture bottle. Visual observations confirmed that stirring inhibited floc formation, while shaking promoted larger flocs compared to the static control condition, which formed smaller flocs and a sheet-like biofilm. Microbial community analysis identified substrate type and degradation progress as primary drivers of community structure, with motion displaying minimal influence. However, metatranscriptomic analysis revealed that motion-induced gene downregulation was associated with motility, surface sensing, and biofilm formation in SAOB and another bacterial species expressing genes for the glycine synthase reductase pathway. Stirring also suppressed oxalate-formate antiporter expression in SPOB, suggesting its dependence on spatial proximity for this energy-conserving mechanism. The strongest gene expression changes of stirring were observed in methanogens, indicating a coupling of the first and last steps of hydrogenotrophic methanogenesis, likely an adaptive strategy for efficient energy conservation. Other downregulated genes included ferrous iron transporters and electron transfer-associated enzymes.

CONCLUSIONS

This study highlights that stirring critically disrupts the initial syntrophic connection between SPOB and methanogens, whereas SAOB communities exhibit greater tolerance to shear stress and disruptive conditions that inhibits aggregate formation. These findings emphasize the importance of carefully managing mixing regimes, especially when attempting to reactivate ammonia-tolerant syntrophic propionate degraders in biogas systems experiencing rapid propionate accumulation under high-ammonia conditions.

Psychrotrophic Antarctic marine bacteria as potential reservoirs for novel antimicrobial genes

Antarctica is a very cold, isolated continent surrounded by frozen seas, yet these extreme environmental conditions have not restricted life and diversity in the sea. The marine environment is seasonally highly productive and harbours diverse and abundant communities of organisms, with many endemic species occurring nowhere else in the world. Such communities and their associated microbiomes are increasingly recognized as an unexplored source of novel antimicrobial products. Hence, the major aim of this study was to examine the antimicrobial potential of bacteria cultured from eight Antarctic marine invertebrate species, while gathering data on Antarctic microbial thermal and salinity tolerances. All cultured bacterial species (n = 34) were related to known psychrotrophs, with thermal tolerances that far exceeded those of their invertebrate hosts. Of note, two strains of Psychrobacter and Pseudomonas produced antagonistic activity towards epidemic methicillin-resistant Staphylococcus aureus, Micrococcus luteus, and Candida albicans in preliminary simultaneous antagonism screens. Draft whole genome sequence analysis revealed the presence of 13 biosynthetic gene clusters; including those with potential to produce betalactones, post-translationally modified peptide products, and arylpropynes. These results emphasize the need for more extensive and systematic surveys to identify novel biomolecules from Antarctic marine bacteria that may be exploited for societal gain.

Nutrient loading accelerates breakdown of refractory dissolved organic carbon in seagrass ecosystem waters

Nutrient loading is a major driver of seagrass ecosystem decline and also threatens the capacity for seagrass ecosystems to act as 'blue carbon' sinks. Dissolved organic carbon (DOC) represents a crucial component of carbon storage in seagrass ecosystems, with refractory DOC (RDOC) playing a key role in long-term (millennial time scale) carbon stocks. The processes governing RDOC are heavily influenced by microbial activity. While it is known that nutrient loading can weaken DOC sequestration potential by changing the DOC composition and transformation, the impact of nutrients on microbial communities that regulate the RDOC pool in seagrass ecosystems remains poorly understood. To address this gap, we conducted a 300-d laboratory incubation experiment to examine the effects of nutrient enrichment on DOC processing and microbial community dynamics. As expected, nutrient addition significantly accelerated the decline in DOC concentration, resulting in the residual DOC exhibiting a higher degree of humification and more depleted δ13C constituents. Concurrent with DOC degradation, microbial community composition shifted from a mix of r- and K-strategists in the early stages to a dominance of K-strategists and fungi in the later stages. Specific bacterial taxa, such as unidentified Rhodospirillales and Oceanococcus, were more prevalent in eutrophicated seagrass waters, while Magnetospira and Nocardioide were more abundant in less eutrophicated waters by the end of the incubation. We speculated that these microbial groups likely adapted to utilise more RDOC, contributing to its decline. The decline in RDOC was approximately 2-times greater in less eutrophicated seagrass waters compared to more eutrophicated waters (26.9 % and 14.5 % decline respectively), which suggests that less eutrophicated seagrass ecosystems are more vulnerable. This study provides evidence that high nutrient loading can enhance RDOC remineralization, ultimately weakening the long-term carbon sequestration potential of seagrass ecosystems.

Geographic factors influence communities of symbiotic bacterial communities in Aphis gossypii across China's major cotton regions

Introduction

Aphids are often infected with diverse bacterial symbionts that enhance their ecological adaptation. While geographic factors significantly influence aphid bacterial communities, research on environmental effects on the cotton aphid Aphis gossypii Glover feeding on cotton plants across China's major cotton-growing regions is limited.

Methods

This study examined the influence of geographic factors on the endosymbiotic bacterial community and diversity of A. gossypii by analyzing 58 field samples from 24 locations across China's major cotton-growing regions (2021-2022) using 16S rRNA (V3-V4) high-throughput sequencing.

Results and discussion

Our results demonstrate that geography is an important factor in shaping the endosymbiotic bacterial composition and diversity of A. gossypii. Among China's three major cotton-growing regions, the Yangtze River Basin exhibited the highest bacterial diversity, followed by the Northwestern Inland Region, and then the Yellow River Basin. Acinetobacter, Lactobacillus, Serratia, and Aeromonas were more abundant in the Yangtze River Basin, with positive correlations observed for Acinetobacter, Serratia, and Aeromonas in relation to annual precipitation. In contrast, Candidatus Uzinura, dominant in southern Xinjiang, displayed negative correlations with precipitation and longitude but a positive correlation with altitude, and this report is the first detection of it in A. gossypii. Buchnera was ubiquitous and negatively associated with both precipitation and temperature, while Arsenophonus showed no significant environmental correlations. These findings highlight the distinct influences of geographic factors on A. gossypii endosymbiotic communities across China's major cotton-growing regions, broadening our understanding of aphid-endosymbiont-environment interactions and offering potential avenues for biocontrol strategies.

Salinity levels influence treatment performance and the activity of electroactive microorganisms in a microbial fuel cell system for wastewater treatment

There is growing interest in developing effective treatment technologies to mitigate the environmental impact of saline wastewater while also potentially recovering valuable resources from it. However, it remains largely unknown how different salinity levels impact treatment performance, energy generation, and the diversity and composition of electroactive microorganisms in MFCs treating real effluents such as urban wastewater. This study explores the impact of three salinity levels (3.5, 7, and 15 g/L NaCl) on current production, organic removal rates, and bacterial community dynamics in a continuous-flow microbial fuel cell (MFC) fed with urban wastewater. Using metagenomics and metatranscriptomics, we explored variations in the abundance and expression of extracellular electron transfer (EET) genes and those involved in other general metabolisms. We found that low salinity (3.5 g/L NaCl) enhanced both current production and organic removal efficiency compared to higher salinity levels. This improvement was linked to an increased abundance and activity of electroactive microorganisms, particularly taxa within the Ignavibacteria class, which possess genes coding for outer membrane cytochromes and porin cytochromes. Additionally, salinity influenced general metabolic genes and microbial community composition, with higher salinity levels limiting bacterial growth and diversity. This research provides valuable insights into the interplay between salinity stress and microbial adaptation, contributing to the optimization of MFC technologies for enhanced environmental and bioengineering applications.

Irrigation Intensities Drive Soil N2O Emission Reduction in Drip-Irrigated Cotton Fields

Drip irrigation with plastic mulch is widely used to save water and improve fertilizer efficiency in arid regions in Xinjiang. However, farmers freely use irrigation water in pursuit of a high cotton yield, and the impact of different irrigation amounts on nitrous oxide (N2O) emissions is still unclear. A field experiment was conducted in 2023 in Xinjiang, China, with drip-irrigated cotton (Gossypium hirsutum L.) to determine N2O emissions with different irrigation intensities. The different irrigation treatments were designed as follows: irrigation was performed to maintain soil moisture at (1) an 80% field capacity (Q80); (2) 90% field capacity (Q90); and (3) 100% field capacity (Q100). The results showed that the yield of cotton decreased with the increase in irrigation intensity. A 100% field capacity is beneficial for ammonium and nitrate transformation. The N2O emissions remained at a relatively low level during the non-irrigated fertilization period. In every irrigation and fertilization cycle, the N2O emissions were mainly concentrated during the process from wet to dry. The peak occurred during days 1-3 of irrigation. Throughout the growth period, the cumulative N2O emissions were 1.15, 1.48, and 2.63 kg N ha-1 under the Q80, Q90, and Q100 treatments, respectively. As the irrigation intensity increased, the dominant species of soil bacteria and fungi showed substitution, while the dominant species of soil actinomycetes were not replaced. Fungi, actinomycetes, the available potassium, and the carbon to nitrogen ratio were positively correlated with nitrous oxide emissions, and the soil temperature was negatively correlated with nitrous oxide emissions. These results demonstrate that increased irrigation could increase the risk of greenhouse gas emissions when using plastic mulch with drip irrigation.

Quantifying patterns of microbial community assembly processes in bioreactors using different approaches leads to variable results

Engineered bioreactors play a vital role in many processes to convert wastes to resources, such as biological wastewater treatment, bioremediation, and conversion of solid waste to methane in landfills. These biological systems rely on communities of microbes to convert waste to valuable resources. A central aspect of the design and operation of bioreactors involves an understanding of microbial community composition and dynamics, including the assembly processes through which they form. However, there remains a significant gap in our fundamental understanding of microbial community dynamics and microbial community assembly (MCA) processes, especially in engineered bioreactor settings. Here, we propose and employ a tool set that can be used by the research community, assess multiple bioreactor systems across a range of process types and ranges, and connect MCA patterns to relevant microbial groups in each bioreactor system. We applied multiple MCA assessment methods using available tools, layering on a trait-based approach, to seven experiments involving different engineered bioreactor systems. The calculated relative contributions of MCA processes varied by the method used, with null modeling approaches estimating a higher influence of stochastic MCA than neutral modeling. While most patterns of MCA were not discernible by general rules, anaerobic generalists assembled more deterministically than anaerobic specialists. Finally, statistical modeling of confidence levels suggests a minimum of 30-40 samples should be used for neutral modeling while a minimum 50-60 samples should be used for null modeling. Overall, we suggest caution when applying and interpreting the results of any one MCA assessment method.

Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon

Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.

Exploring the interplay of under-deposit corrosion and microbiologically influenced corrosion in the presence of deposits with varied electrical conductivities

In oil and gas pipelines, the coexistence of native microorganisms with various solid compounds, such as corrosion products, scales, and reservoir sand, is well-established. However, research focused on understanding the collective impact of these components on carbon steel corrosion has been limited, with most studies concentrating on inert deposits like clay and sand. This study assessed the impact of electrically conductive deposits - magnetite (Fe3O4) and troilite (FeS) - on UDC and UDMC of carbon steel, employing silica (SiO2) as an inert control. A multifaceted approach, combining international corrosion standards, microscopy, and molecular microbiology techniques demonstrated that abiotic corrosion rates correlated with the electrical conductivity of the deposits. Magnetite, the deposit with the highest electrical conductivity, led to the highest uniform corrosion rate (0.110 mm/year). The troilite-containing reactor exhibited a corrosion rate of 0.017 mm/year, while the lowest rate was observed in the presence of sand (0.006 mm/year), the deposit with the lowest electrical conductivity. In biotic conditions, the highest average corrosion and pitting rates were also associated with magnetite, identifying UDC and UDMC in the presence of magnetite as the most corrosive scenario among the three deposits. Nevertheless, the average corrosion and pitting rates did not follow the same trend as in abiotic conditions, where electrical conductivity properties governed the behaviour. In biotic conditions, the heightened pitting corrosion observed in the presence of silica over troilite was attributed to higher metabolic activity and increased cell concentrations in the microbial consortium under this scenario. These findings underscore the complexity of UDMC, suggesting that an active microbial consortium does not solely drive severe corrosion but is influenced by multiple factors. This study offers insights into the role of different deposits and native microbial communities, paving the way for more targeted corrosion mitigation strategies to improve infrastructure longevity in oil and gas systems.

Advantageous effects of rumen-protected phytonutrients from tropical plant extracts on rumen fermentation efficiency and methane mitigation using in vitro fermentation technique

OBJECTIVE

Tropical plants are composed of phytonutrients (PTNs) and are utilized for their capacity to manipulate rumen fermentation characteristics and methane production. The aim of this experiment was to determine the impact of microencapsulated PTNs-extracted from lemongrass and mangosteen peel (M-LEMANGOS), as well as crude protein (CP) levels on nutrient degradability, rumen ecology, microbial population, and methane emission in an in vitro study.

METHODS

The treatments were randomly assigned in a 2×4 Factorial arrangement in a completely randomized design. The two factors consisted of CP percentage in the concentrate diet (16% and 18% CP) and the levels of M-LEMANGOS addition (0%, 2%, 4%, and 6% of the total substrate).

RESULTS

The results showed that nutrient degradability both 12 and 24 h were significantly increased with M-LEMANGOS at 4% total substate. In part of volatile fatty acids (VFAs), particularly propionate and total VFA, these were enhanced by %CP and M-LEMANGOS combination. The %CP increased ruminal ammonia-nitrogen concentration (NH3-N), while M-LEMANGOS supplementation reduced such concentration. Methane production and Methanobacteriales population at 12 and 24 h were reduced when supplemented with M-LEMANGOS at 4% total substate. The population of Fibrobacter succinogenes, Ruminococcus flavefaciens, and Megasphaera elsdenii were increased with the interaction between %CP and M-LEMANGOS addition.

CONCLUSION

M-LEMANGOS indicates promising potential as a plant-based PTN for dietary modulation of rumen fermentation and mitigation of methane production.

A robust strategy for overexpression of DNA polymerase from Thermus aquaticus using an IPTG-independent autoinduction system in a benchtop bioreactor

The DNA polymerase derived from Thermus aquaticus is the most widely utilized among various DNA polymerases, indicating its significant economic importance. Consequently, efforts to achieve a substantial yield of Taq DNA polymerase (Taq-pol) are ongoing. The expression of recombinant protein using T7-induced promoters presents challenges in cost-effectiveness, primarily due to the reliance on traditional induction method. Our study aims to enhance cost-efficiency, and scalability of our method for overproducing Taq-pol, particularly in comparison to traditional IPTG-induced techniques, which remain underreported in the current literature. To achieve those purposes, this work integrated the use of (1) a high copy number vector; (2) an optimized chemically defined medium; and (3) optimized fermentation conditions in a 5 L bioreactor. A total of 83.5 mg/L of pure Taq-pol was successfully synthesized in its active form, leading to a 9.7-fold enhancement in protein yield. This was achieved by incorporating glucose, glycerol, and lactose into a defined medium at concentrations of 0.1, 0.6, and 1%, respectively, under specific production conditions in a 5 L bioreactor: 300 rpm, 2 vvm, and 10% inoculant. The data collectively suggest that the strategy serves as a significant foundation for the future advancement of large-scale production of Taq-pol.

Study of Bacterial Communities in Water and Different Developmental Stages of Aedes aegypti from Aquatic Breeding Sites in Leticia City, Colombian Amazon Biome

Aedes aegypti is a key vector in the transmission of arboviral diseases in the Colombian Amazon. This study aimed to characterize microbiota composition using DNA extracted from water in artificial breeding sites, immature stages, and adults of Ae. aegypti in Leticia, Amazonas. Additionally, the physicochemical water variables were correlated with the bacterial communities present. Eight artificial breeding sites were identified, with bucket, plant pot, and tire being the most frequent. The breeding sites exhibited similar physicochemical profiles, with significant temperature and salinity differences (p-value < 0.03). The most representative bacterial genera included Ottowia (82%), Xanthobacter (70.59%), and Rhodocyclaceae (92.78%) in breeding site water; Aquabacterium (61.07%), Dechloromonas (82.85%), and Flectobacillus (58.94%) in immature stages; and Elizabethkingia (70.89%) and Cedecea (39.19%) in males and females of Ae. aegypti. Beta diversity analysis revealed distinct clustering between adults and the water and immature communities (p-value < 0.001). Multivariate analysis showed strong correlations among bacterial communities, breeding sites, and physicochemical variables such as tire and drum cover which exhibited high levels of total dissolved solids, conductivity, and salinity associated with Flectobacillus, Leifsonia, Novosphingobium, Ottowia, and Rhodobacter. Bacterial genera such as Mycobacterium, Escherichia, Salmonella, and Clostridium, present in artificial breeding sites, are associated with public health relevance. This study provides insights into bacterial community dynamics across Ae. aegypti's life cycle and underscores the importance of water physicochemical and biological characteristics for developing new vector control strategies.

In Vitro Investigation of the Effects of Bacillus subtilis-810B and Bacillus licheniformis-809A on the Rumen Fermentation and Microbiota

Direct-fed microbials (DFMs) have shown the potential to improve livestock performance and overall health. Extensive research has been conducted to identify new DFMs and understand their mechanisms of action in the gut. Bacillus species are multifunctional spore-forming bacteria that exhibit resilience to harsh conditions, making them ideal candidates for applications in the feed industry and livestock production. This study investigates the mode of action of B. licheniformis and B. subtilis in the rumen using diverse in vitro techniques. Our results revealed that both strains germinated and grew in sterile rumen and intestinal contents from dairy cows and bulls. Gas composition analysis of in vitro cultures in a medium containing 40% rumen fluid demonstrated that germination of B. licheniformis and B. subtilis strains reduced oxygen levels, promoting an anaerobic environment favorable to rumen microbes. Enzymatic activity assays showed that B. licheniformis released sugars from complex substrates and purified polysaccharides in filtered rumen content. Additionally, the combination of B. licheniformis and B. subtilis survived and grew in the presence of a commercial monensin dose in rumen fluid media. The effects of B. licheniformis and B. subtilis on rumen fermentation activity and microbiota were studied using an in vitro batch fermentation assay. In fermenters that received a combination of B. licheniformis and B. subtilis, less CO2 was produced while dry matter degradation and CH4 production was comparable to the control condition, indicating better efficiency of dry matter utilization by the microbiota. The investigation of microbiota composition between supplemented and control fermenters showed no significant effect on alpha and beta diversity. However, the differential analysis highlighted changes in several taxa between the two conditions. Altogether, our data suggests that the administration of these strains of Bacillus could have a beneficial impact on rumen function, and consequently, on health and performance of ruminants.

Changes in bacterial diversity of full-scale anaerobic digesters treating secondary sludge

Anaerobic digestion (AD) of secondary sludge (2S) presents challenges because of its high microbial content and complex cell wall structures. The purpose of this study was to investigate the effects of spatiotemporally-variable factors such as water temperature and dietary habits on the 2S bacterial community and its migration into digesters. Bacterial communities and functions were analyzed using high-throughput pyrosequencing. Spatiotemporal variations in bacterial populations were identified, with genera such as Zoogloea and Dechloromonas migrating into digesters and influencing organic degradation. Notably, Zoogloea was negatively correlated with VS removal, potentially due to cell floc formation, whereas Dechloromonas was positively correlated, suggesting its role in acetate metabolism anaerobically. This study emphasizes the importance of microbial migration from 2S to digesters, highlighting the need to monitor microbial communities along with conventional parameters to increase AD performance. These findings provide practical insights into optimizing sludge management and improving biogas production in AD plants.

Highly Dynamic Archaeal and Bacterial Communities From the Surface to the Deep in the Atlantic Ocean

Though archaea are ubiquitous in the oceans, at times present in quantities equal to bacteria, in general, archaea are underreported when compared with bacteria, and little is known about archaeal connectivity in the ocean. Here, we present the first time series data of size-fractionated archaea with temporal resolution of days across a depth transect in the oligotrophic Atlantic Ocean. Archaeal communities were variable from day to day, both in regards to community composition and relative abundance. In the context of the total prokaryotic community, we found that water depth and particle size were both determinants of the archaeal share of microbial populations, though the archaeal portion of the community was less discriminating between size and depth classes than the rest of the community. Quantitative PCR shows lower relative abundances of archaea in the deep Atlantic Ocean than previously reported. Overall, we find far lower connectivity between depths in the Atlantic Ocean than suggested by previous studies.

Assessing the impact of sewage and wastewater on antimicrobial resistance in nearshore Antarctic biofilms and sediments

BACKGROUND

Despite being recognised as a global problem, our understanding of human-mediated antimicrobial resistance (AMR) spread to remote regions of the world is limited. Antarctica, often referred to as "the last great wilderness", is experiencing increasing levels of human visitation through tourism and expansion of national scientific operations. Therefore, it is critical to assess the impact that these itinerant visitors have on the natural environment. This includes monitoring human-mediated AMR, particularly around population concentrations such as visitor sites and Antarctic research stations. This study takes a sequencing discovery-led approach to investigate levels and extent of AMR around the Rothera Research Station (operated by the UK) on the Antarctic Peninsula.

RESULTS

Amplicon sequencing of biofilms and sediments from the vicinity of Rothera Research Station revealed highly variable and diverse microbial communities. Analysis of AMR genes generated from long-reads Nanopore MinION sequencing showed similar site variability in both drug class and resistance mechanism. Thus, no site sampled was more or less diverse than the other, either in the biofilm or sediment samples. Levels of enteric bacteria in biofilm and sediment samples were low at all sites, even in biofilm samples taken from the station sewage treatment plant (STP). It would appear that incorporation of released enteric bacteria in wastewater into more established biofilms or associations with sediment was poor. This was likely due to the inactivation and vulnerability of these bacteria to the extreme environmental conditions in Antarctica.

CONCLUSIONS

Our results suggest minimal effect of a strong feeder source (i.e. sewage effluent) on biofilm and sediment microbial community composition, with each site developing its unique niche community. The factors producing these niche communities need elucidation, alongside studies evaluating Antarctic microbial physiologies. Our data from cultivated bacteria show that they are highly resilient to different environmental conditions and are likely to thrive in a warmer world. Our data show that AMR in the Antarctic marine environment is far more complex than previously thought. Thus, more work is required to understand the true extent of the Antarctic microbiota biodiversity, their associated resistomes and the impact that human activities have on the Antarctic environment.

Trees shape the soil microbiome of a temperate agrosilvopastoral and syntropic agroforestry system

Agroforestry systems are multifunctional land-use systems that promote soil life. Despite their large potential spatio-temporal complexity, the majority of studies that investigated soil organisms in temperate cropland agroforestry systems focused on rather non-complex systems. Here, we investigated the topsoil and subsoil microbiome of two complex and innovative alley cropping systems: an agrosilvopastoral system combining poplar trees, crops, and livestock and a syntropic agroforestry system combining 35 tree and shrub species with forage crops. Increasing soil depth resulted in a decline of bacterial and fungal richness and a community shift towards oligotrophic taxa in both agroforestry systems, which we attribute to resource-deprived conditions in subsoil. At each soil depth, the microbiome of the tree rows was compositionally distinct from the crop rows. We detected a shift towards beneficial microorganisms as well as a decline in putative phytopathogens under the trees as compared to the crop rows. Finally, based on our results on community dissimilarity, we found that compared to an open cropland without trees, spatial heterogeneity introduced by the tree rows in the agrosilvopastoral system translated into a compositionally less homogeneous soil microbiome, highlighting the potential of agroforestry to counteract the homogenization of the soil microbiome through agriculture.

Human Milk Archaea Associated with Neonatal Gut Colonization and Its Co-Occurrence with Bacteria

Archaea have been identified as early colonizers of the human intestine, appearing from the first days of life. It is hypothesized that the origin of many of these archaea is through vertical transmission during breastfeeding. In this study, we aimed to characterize the archaeal composition in samples of mother-neonate pairs to observe the potential vertical transmission. We performed a cross-sectional study characterizing the archaeal diversity of 40 human colostrum-neonatal stool samples by next-generation sequencing of V5-V6 16S rDNA libraries. Intra- and inter-sample analyses were carried out to describe the Archaeal diversity in each sample type. Human colostrum and neonatal stools presented similar core microbiota, mainly composed of the methanogens Methanoculleus and Methanosarcina. Beta diversity and metabolic prediction results suggest homogeneity between sample types. Further, the co-occurrence network analysis showed associations between Archaea and Bacteria, which might be relevant for these organisms' presence in the human milk and neonatal stool ecosystems. According to relative abundance proportions, beta diversity, and co-occurrence analyses, the similarities found imply that there is vertical transmission of archaea through breastfeeding. Nonetheless, differential abundances between the sample types suggest other relevant sources for colonizing archaea to the neonatal gut.

Impact of trace elements (total and labile fraction) on the anaerobic digestion activity and microbial community structure

Trace elements (TEs) in anaerobic digestion (AD) are known to be essential for optimal biogas production, but inhibitive in excessive concentrations. However, the mechanisms of inhibition are not fully understood. The effects of the addition essential TEs (Co, Cu and Ni) and a non-essential TE (Cd) on the microbial community structure of AD were studied in lab-scale reactors, using total TE concentrations that ranged from 0 to 100 μM. Reactor performance was assessed by monitoring biogas production. The labile fraction of TEs (the most bioaccessible species) was determined by diffusive gradients in thin-films technique. Prokaryotic community composition was characterized through high throughput sequencing (HTS) targeting archaea and bacteria and qPCR to evaluate changes in methanogens and metal resistance genes. Only a minor fraction of added TEs was labile and it decreased over time, with Ni being the most labile. Although only a minor fraction of spiked concentration was labile, all TEs inhibited biogas production at the highest spiking concentration (100 μM), with higher inhibition observed for Cd and Ni. HTS and qPCR revealed changes, particularly in archaea, with reduced relative abundance at higher TE concentrations. Shifts in prokaryotic communities suggest alterations in AD metabolic pathways. High inhibition of biogas was linked to reduced diversity, dominance of the bacterial genus Klebsiella and changes in the ratio acetoclastic / hydrogenotrophic methanogens. This study addresses a research gap in understanding how TEs inhibit AD, and provides a strategy to improve TE dosing by monitoring the labile fraction of TEs to avoid overdosing.

Effects of prebiotics from diverse sources on dysbiotic gut microbiota associated to western diet: Insights from the human Mucosal ARtificial COLon (M-ARCOL)

Associated to various illnesses, Western Diet (WD) is acknowledged to have deleterious effects on human gut microbiota, decreasing bacterial diversity, lowering gut bacteria associated to health (such as Akkermansia muciniphila), while increasing those linked to diseases (e.g., Proteobacteria). In this study, we evaluated the potential of two new prebiotics to counteract the negative effect of WD on gut microbiota, namely raffinose family oligosaccharides (RFO) from chickpeas and laminarin (LAM) from algae, when compared to the well-known inulin (INU). The effects of prebiotics on gut microbiota composition and metabolic activities were investigated in the Mucosal-Artificial Colon, set-up to reproduce WD condition, as compared to healthy control (n = 3). None of the prebiotics was able to efficiently offset the shift in microbiota induced by WD. Nevertheless, when compared to non-supplemented WD, all prebiotics showed significant impacts on microbiota composition, that were both prebiotic and donor-dependant. RFO was the only prebiotic to enhance α-diversity, while it led to an increase in Blautia and Butyricicoccaceae, associated with higher amounts of gas and butyrate. LAM and INU did not strongly impact microbial metabolic activities but were associated with a rise in Prevotella_9/Agathobacter and Faecalibacterium, respectively. To conclude, this study showed that all tested prebiotics had different impacts on human gut microbiota structure and activities, which was further donor-dependent. M-ARCOL appears as a suitable in vitro tool to better understand the mechanisms of action of prebiotic compounds in relation to gut microbes and define responders and non-responders to prebiotic supplementation, opening the possibility of customized nutritional strategies.

Microbial landscapes in Trinervitermes trinervoides termite colonies are affected by mound compartments and soil properties but not by symbiotic Podaxis fungi

Termites are important ecosystem engineers and play key roles in modulating microbial communities within and outside their mounds. Microbial diversity within termite mounds is generally lower than surrounding soils, due to termite-associated antimicrobial compounds and active sanitary behaviours. Microbial symbionts of termites can also influence the microbial landscape, by inhibiting or out-competing other microbes. Certain members of the arid habitat fungal genus Podaxis (Agaricomycetes; Agaricaceae) are symbiotic with savannah specialist grass-cutting termites, and have the potential to influence mound-associated microbiomes. To test this, we characterized fungal (ITS2) and bacterial (16S rRNA) communities within and outside 49 Trinervitermes trinervoides mounds with and without Podaxis fruiting bodies across a 1000 km transect in South Africa. We predicted that Podaxis would be a dominant member of the fungal communities in mounds and negatively impact microbial diversity. Further, we explored how environmental variables shaped microbial communities, including whether soil elemental composition affected Podaxis presence. As expected, we observed less diverse fungal communities, but not bacterial communities, within than outside mounds, while microbial communities differed by sampling regions and mound compartments. Podaxis sequences were present in 48 out of 49 mounds in low relative abundances, and neither fruiting body presence nor sequence abundance were associated with microbial diversity or composition. There was, however, an overall association between the presence of Podaxis fruiting bodies and elemental composition, with different elements displaying varying associations depending on geographic region. Both environmental variables and soil elements were associated with fungal and bacterial taxa, indicating that they are key drivers of microbial community composition. Taken together, our findings suggest that microbial landscapes in termite mounds are not strongly influenced by Podaxis but mainly driven by termite filtering and regional abiotic variables and elemental compositions.

Abundance and composition data of microbiomes in agricultural biogas plants of Lower Saxony, Germany, with variation in organic substrates, process parameters and nutrients

This article presents high-throughput DNA sequencing, quantitative PCR data of microbial communities, and process parameters as recovered from eight biogas plants (BPs) located in Lower Saxony, Germany. Samples were collected from both the main (MD) and secondary digesters (SD). Additionally, for 4 BPs, samples were also obtained from the residue digester storage (RDS). Different BPs employed various types of substrates originating from cattle manure, chicken manure, pig manure, or renewable resources. Information on physico-chemical process parameters and concentrations of macro- and micro-nutrients in the BPs is provided. Total DNA from all samples were extracted using a phenol-chloroform-based method. To determine the abundance of bacteria and archaea, their 16S rRNA genes were quantified by real-time PCR (qPCR), and to characterize their community composition, paired-end DNA sequence reads were generated from PCR amplicons with Illumina MiSeq. All statistical analyses were performed in R to explore the microbial diversity, abundance, and community structure among different BPs and digesters (MD, SD, RDS). The presence and distribution of the major bacterial and archaeal phyla indicated for each BP unique and diverse microbial communities with typically higher bacterial than archaeal abundances.

Large intestinal nutritional and physicochemical parameters from different dog sizes reshape canine microbiota structure and functions in vitro

Different dog sizes are associated with variations in large intestinal physiology including gut microbiota, which plays a key role in animal health. This study aims to evaluate, using the CANIM-ARCOL (Canine Mucosal Artificial Colon), the relative importance of gut microbes versus physicochemical and nutritional parameters of the canine colonic environment in shaping microbiota structure and functions. CANIM-ARCOL was set up to reproduce nutrient availability, bile acid profiles, colonic pH, and transit time from small, medium, or large dogs according to in vivo data, while bioreactors were all inoculated with a fecal sample collected from medium size dogs (n = 2). Applying different dog size parameters resulted in a positive association between size and gas or SCFA production, as well as distinct microbiota profiles as revealed by 16S Metabarcoding. Comparisons with in vivo data from canine stools and previous in vitro results obtained when CANIM-ARCOL was inoculated with fecal samples from three dog sizes revealed that environmental colonic parameters were sufficient to drive microbiota functions. However, size-related fecal microbes were necessary to accurately reproduce in vitro the colonic ecosystem of small, medium, and large dogs. For the first time, this study provides mechanistic insights on which parameters from colonic ecosystem mainly drive canine microbiota in relation to dog size. The CANIM-ARCOL can be used as a relevant in vitro platform to unravel interactions between food or pharma compounds and canine colonic microbiota, under different dog size conditions. The potential of the model will be extended soon to diseased situations (e.g. chronic enteropathies or obesity).

Stand age-related effects of mangrove on archaeal methanogenesis in sediments: Community assembly and co-occurrence patterns

Mangrove sediment is a key source of methane emissions; however, archaea community structure dynamics and methanogenesis activities during long-term mangrove restoration remain unclear. In this study, microcosm incubations revealed a substantial reduction in microbial-mediated methane production potential from mangrove sediments with increasing stand age; methane production rates decreased from 0.42 ng g-1 d-1 in 6-year-old stands to 0.23 ng g-1 d-1 in 64-year-old stands. High-throughput sequencing revealed a reduction in community diversity because of specific microorganism colonization and species loss, notably a decline in the relative abundance of Bathyarchaeia in sediments of 64-year-old stands. In addition, mangrove sediments, especially those in older stands (20- and 64-year-old), had more complex and stable co-occurrence microbial networks than mudflats. Furthermore, archaea community assembly in older stands was dominated by stochastic processes wherein dispersal limitation was prominent, and that in younger stands (6- and 12-year-old) was driven by deterministic processes. The proportion of dispersal limitation of Bathyarchaeia and traditional methanogens in sediment decreased with an increase in stand age. Quantitative polymerase chain reaction analysis confirmed a decrease in Bathyarchaeia (from 3.50 to 0.54 copies g-1) and mcrA gene (from 3.83 to 0.25 copies g-1) abundance in mangrove sediments with an increase in stand age. These findings demonstrate the critical role of Bathyarchaeia in methanogenesis; the decline in microbial interactions and abundance, and the reduced proportion of dispersal limitation of Bathyarchaeia and traditional methanogens collectively contributed to the mitigation of microbial-mediated methane production potential in older mangrove stands.

Genomic variability in Zika virus in GBS cases in Colombia

Major clusters of Guillain-Barré Syndrome (GBS) emerged during the Zika virus (ZIKV) outbreaks in the South Pacific and the Americas from 2014 to 2016. The factors contributing to GBS susceptibility in ZIKV infection remain unclear, although considerations of viral variation, patient susceptibility, environmental influences, and other potential factors have been hypothesized. Studying the role of viral genetic factors has been challenging due to the low viral load and rapid viral clearance from the blood after the onset of Zika symptoms. The prolonged excretion of ZIKV in urine by the time of GBS onset, when the virus is no longer present in the blood, provides an opportunity to unravel whether specific ZIKV mutations are related to the development of GBS in certain individuals. This study aimed to investigate the association between specific ZIKV genotypes and the development of GBS, taking advantage of a unique collection of ZIKV-positive urine samples obtained from GBS cases and controls during the 2016 ZIKV outbreak in Colombia. Utilizing Oxford-Nanopore technology, we conducted complete genome sequencing of ZIKV in biological samples from 15 patients with GBS associated with ZIKV and 17 with ZIKV infection without neurological complications. ZIKV genotypes in Colombia exhibited distribution across three clades (average bootstrap of 90.9±14.9%), with two clades dominating the landscape. A comparative analysis of ZIKV genomes from GBS and non-neurological complications, alongside 1368 previously reported genomes, revealed no significant distinctions between the two groups. Both genotypes were similarly distributed among observed clades in Colombia. Furthermore, no variations were identified in the amino acid composition of the viral genome between the two groups. Our findings suggest that GBS in ZIKV infection is perhaps associated with patient susceptibility and/or other para- or post-infectious immune-mediated mechanisms rather than with specific ZIKV genome variations.

Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays

Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed. KEY POINTS: • The applied methodology was successful to obtain biomass suitable to perform BMP assays. • The microbial community was resilient to external biomass addition. • Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.

Microbial education plays a crucial role in harnessing the beneficial properties of microbiota for infectious disease protection in Crassostrea gigas

The increase in marine diseases, particularly in economically important mollusks, is a growing concern. Among them, the Pacific oyster (Crassostrea gigas) production faces challenges from several diseases, such as the Pacific Oyster Mortality Syndrome (POMS) or vibriosis. The microbial education, which consists of exposing the host immune system to beneficial microorganisms during early life stages is a promising approach against diseases. This study explores the concept of microbial education using controlled and pathogen-free bacterial communities and assesses its protective effects against POMS and Vibrio aestuarianus infections, highlighting potential applications in oyster production. We demonstrate that it is possible to educate the oyster immune system by adding microorganisms during the larval stage. Adding culture based bacterial mixes to larvae protects only against the POMS disease while adding whole microbial communities from oyster donors protects against both POMS and vibriosis. The efficiency of immune protection depends both on oyster origin and on the composition of the bacterial mixes used for exposure. No preferential protection was observed when the oysters were stimulated with their sympatric strains. Furthermore, the added bacteria were not maintained into the oyster microbiota, but this bacterial addition induced long term changes in the microbiota composition and oyster immune gene expression. Our study reveals successful immune system education of oysters by introducing beneficial microorganisms during the larval stage. We improved the long-term resistance of oysters against critical diseases (POMS disease and Vibrio aestuarianus infections) highlighting the potential of microbial education in aquaculture.

Biofilm growth dynamics in a micro-irrigation with reclaimed wastewater in the field scale

The dripper clogging due to the development of biofilm can reduce the benefits of micro-irrigation technology implementation using reclaimed wastewater. The narrow cross-section and labyrinth geometry of the dripper channel enhance the fouling mechanisms. The aim of this study was to evaluate the water distribution and biofouling of drip irrigation systems at the field scale during irrigation with treated wastewater. Six 100 m lines of commercial pipes with two pressure-compensating dripper types (flow rate, Q, of 0.65 L h-1 and 1.5 L h-1, respectively) were monitored for four months. Different zones along the pipes were selected to evaluate the influence of hydrodynamical conditions (Reynolds number = 5400 to 0) on biofouling. Destructive methods involving the biofilm extraction by mechanical means, showed little biofilm development without significant differences in dry and organic matter content in function of the sampling location along the pipe or dripper flow rate (Q0.65 and Q1.5). These results were confirmed by non-destructive methods, such as optical coherence tomography, that nevertheless showed that biofouling concerned 15-20% of the total dripper labyrinth volume. Total organic carbon monitoring and its composition (by three-dimensional excitation and emission matrix fluorescence microscopy) showed that the biofilm did not significantly influence the organic matter nature. Our results indicated that the biological activity and biofilm development in irrigation systems were more affected by the environmental conditions, particularly water temperature, rather than flow conditions. This confirmed that treated wastewater with low organic content can be used in micro-irrigation systems without significant loss of efficiency, even in conditions requiring intensive irrigation, such as the Mediterranean climate.

Spatiotemporal dynamics of dinoflagellate communities in the Taiwan Strait and their correlations with micro-eukaryotic and bacterial communities

Dinoflagellate blooms have negative adverse effects on marine ecosystems. However, our knowledge about the spatiotemporal distribution of dinoflagellate communities and their correlations with micro-eukaryotic and bacterial communities is still rare. Here, the sediment micro-eukaryotic and bacterial communities were explored in the Taiwan Strait (TWS) by 16S and 18S rRNA gene high-throughput sequencing. We found that the dinoflagellates were the most abundant algal group in TWS, and their relative abundance was higher in spring and autumn than in summer. Moreover, the species richness and community composition of dinoflagellates showed strong seasonal patterns. NO3-N and NH4-N had the strongest correlations with the spatiotemporal dynamics of community composition of dinoflagellates. The dinoflagellates had a significantly wider niche breadth than other algal groups for NH4-N, NO3-N and NO2-N, and therefore potentially contributed to a wider distribution range and high abundance in TWS. In addition, the dinoflagellates had stronger impacts on microeukaryotes than on bacteria for both community composition and species richness. However, the dinoflagellates showed close coexistence with bacteria but loose coexistence with microeukaryotes in spring co-occurrence networks. This close coexistence suggests the potentially strong synergy effects between dinoflagellates and bacteria in spring dinoflagellate blooms in TWS. Overall, this study revealed the distribution mechanisms of dinoflagellates in TWS based on niche breadth and also unveiled the different effects of dinoflagellates on micro-eukaryotic and bacterial communities.

Bioefficiency of microencapsulated hemp leaf phytonutrient-based extracts to enhance in vitro rumen fermentation and mitigate methane production

The objective was to assess the supplementation with microencapsulation of hemp leaf extract (mHLE) utilized as a rumen enhancer on in vitro rumen fermentation and to enhance the bioavailability of active compounds for antimicrobial action, particularly in protozoa and methanogen populations. The feed treatments were totally randomized in the experimental design, with different levels of mHLE diet supplemented at 0, 4, 6 and 8% of total DM substrate and added to an R:C ratio of 60:40. During fermentation, gas kinetics production, nutrient degradability, ammonia nitrogen concentration, volatile fatty acid (VFA) profiles, methane production, and the microbial population were measured. The supplemented treatment at 6% of total DM substrate affected reductions in gas kinetics, cumulative gas production, and volatile fatty acid profiles, especially the acetate and acetate to propionate ratio. Whereas propionate proportion and total volatile fatty acid concentration were enhanced depending on the increase of nutrients in vitro dry matter degradability (IVDMD) after 12 h of post-fermentation at a R:C ratio of 60:40 (P < 0.05). Consequently, mHLE addition resulted in optimal ruminal pH and increased nutrient degradability, followed by ammonia nitrogen concentrations (P < 0.05), which were enhanced by dominant cellulolytic bacteria, particularly Ruminococcus albus and Ruminococcus flavefaciens, which showed the highest growth rates in the rumen ecology. Therefore, mHLE, a rich phytonutrient feed additive, affected the methanogen population, reduced the calculated methane production and can be a potential supplement in the ruminant diet.

The interplay between host-specificity and habitat-filtering influences sea cucumber microbiota across an environmental gradient of pollution

Environmental gradients can influence morpho-physiological and life-history differences in natural populations. It is unclear, however, to what extent such gradients can also modulate phenotypic differences in other organismal characteristics such as the structure and function of host-associated microbial communities. In this work, we addressed this question by assessing intra-specific variation in the diversity, structure and function of environmental-associated (sediment and water) and animal-associated (skin and gut) microbiota along an environmental gradient of pollution in one of the most urbanized coastal areas in the world. Using the tropical sea cucumber Holothuria leucospilota, we tested the interplay between deterministic (e.g., environmental/host filtering) and stochastic (e.g., random microbial dispersal) processes underpinning host-microbiome interactions and microbial assemblages. Overall, our results indicate that microbial communities are complex and vary in structure and function between the environment and the animal hosts. However, these differences are modulated by the level of pollution across the gradient with marked clines in alpha and beta diversity. Yet, such clines and overall differences showed opposite directions when comparing environmental- and animal-associated microbial communities. In the sea cucumbers, intrinsic characteristics (e.g., body compartments, biochemistry composition, immune systems), may underpin the observed intra-individual differences in the associated microbiomes, and their divergence from the environmental source. Such regulation favours specific microbial functional pathways that may play an important role in the survival and physiology of the animal host, particularly in high polluted areas. These findings suggest that the interplay between both, environmental and host filtering underpins microbial community assembly in H. leucospilota along the pollution gradient in Hong Kong.

Disruption of millipede-gut microbiota in E. pulchripes and G. connexa highlights the limited role of litter fermentation and the importance of litter-associated microbes for nutrition

Millipedes are thought to depend on their gut microbiome for processing plant-litter-cellulose through fermentation, similar to many other arthropods. However, this hypothesis lacks sufficient evidence. To investigate this, we used inhibitors to disrupt the gut microbiota of juvenile Epibolus pulchripes (tropical, CH4-emitting) and Glomeris connexa (temperate, non-CH4-emitting) and isotopic labelling. Feeding the millipedes sterile or antibiotics-treated litter reduced faecal production and microbial load without major impacts on survival or weight. Bacterial diversity remained similar, with Bacteroidota dominant in E. pulchripes and Pseudomonadota in G. connexa. Sodium-2-bromoethanesulfonate treatment halted CH4 emissions in E. pulchripes, but it resumed after returning to normal feeding. Employing 13C-labeled leaf litter and RNA-SIP revealed a slow and gradual prokaryote labelling, indicating a significant density shift only by day 21. Surprisingly, labelling of the fungal biomass was somewhat quicker. Our findings suggest that fermentation by the gut microbiota is likely not essential for the millipede's nutrition.

Discovery of a Microbial Carrier with High Adsorption Affinity for Syntrophic Long-Chain Fatty Acid-Degrading Microorganisms

Long-chain fatty acid (LCFA) degradation primarily involves several species of Syntrophomonas and hydrogenotrophic methanogens, constituting the rate-limiting step in anaerobic digestion. It is crucial to augment their abundance to enhance LCFA degradation. Utilizing microbial carriers presents an effective strategy to maintain the microorganisms on the surface and prevent their washout from the digester. In this study, we aimed to identify a suitable microbial carrier with a superior adsorption capacity for LCFA-degrading microorganisms. We tested various polymers, poly(vinyl alcohol) (PVA), polypropylene (PP), polyethylene glycol (PEG), and polyvinylidene chloride (PVDC), adding them to the sludge at the concentration of 28.25 g L-1 and incubating with olive oil. The amplicon sequencing analysis revealed that PVDC retained Syntrophomonas more abundantly than the other polymers. Remarkably, PVDC predominantly adsorbed LCFA-degrading S. sapovorans and S. zehnderi, whereas medium- to short-chain fatty acid-degrading S. wolfei was abundant in the sludge. Moreover, hydrogenotrophic Methanospirillum hungatei was detected at 2.3-9.5 times higher abundance on PVDC compared to the sludge. Further analysis indicated that not only these LCFA-degrading syntrophic microbial communities but also Propionispira and Anaerosinus, which are capable of lipid hydrolysis and glycerol degradation, became dominant on PVDC. Actually, chemical analysis confirmed that adding PVDC promoted the olive oil degradation. These results underscore the potential of PVDC in promoting anaerobic LCFA degradation.

Efficacy of zinc nanoparticle supplementation on ruminal environment in lambs

BACKGROUND

Zinc nanoparticles (NPs) are characterized by high bioavailability, small size, and high absorbability. The purpose of this experiment was to determine the effect of Zn-NP feed supplementation on ruminal fermentation, microbiota, and histopathology in lambs. In vitro (24 h), short-term (STE, 28 d), and long-term (LTE, 70 d) experiments were performed. The lambs in STE were fed a basal diet (BD) composed of 350 g/d ground barley and 700 g/d meadow hay (Control), BD enriched with ZnO-NPs (80 mg Zn/kg of diet, ZnO-NPs), and BD enriched with Zn phosphate-based NPs (80 mg Zn/kg of diet, ZnP-NP). The in vitro gas production technique was used in incubated rumen fluid from STE. The lambs in LTE were fed BD (Control), BD enriched with ZnO-NPs (40 mg Zn/kg of diet, ZnO-NP40), BD enriched with ZnO-NPs (80 mg Zn/kg of diet, ZnO-NP80) and BD enriched with ZnO (80 mg Zn/kg of diet, ZnO-80).

RESULTS

After 24 h of incubation, dry matter digestibility was higher for ZnO-NP and ZnP-NP substrates than the control in an in vitro experiment (P < 0.001). The total bacterial population in the STE was lower (P < 0.001) in the ZnP-NP group than in the control and ZnO-NP groups, but the protozoan populations were not significantly different. The ammonia-N concentration in LTE was lowest in the ZnO-NP80 group (P = 0.002), but the activities of carboxymethyl cellulase (P < 0.001) and xylanase (P = 0.002) were higher in the ZnO-NP40, ZnO-NP80, and ZnO-80 groups than in the control group. Morphological observation after STE and LTE revealed histological changes (e.g. inflammation of the epithelium or edema of the connective tissue) in the rumen of lambs.

CONCLUSION

Zn-NP supplementation up to 70 d improved feed-use efficiency and influenced ammonia-N concentration and activities of hydrolases in the rumen. The active ruminal fermentation affected the health of the ruminal papillae and epithelium in the lambs, regardless of the application's form, dose, or duration. However, by affecting rumen microbial fermentation, Zn-NPs could alter fermentation patterns, thereby increasing the capacity of host rumen epithelial cells to transport short-chain fatty acids.

Delayed Shift in Microbiota Composition in a Marine Microcosm Pollution Experiment

Benthic habitats are the largest habitats on Earth, being essential for marine ecosystem functioning. Benthic habitats are particularly vulnerable towards pollution and anthropogenetic influence due to general oligotrophic nature. We, therefore, simulated pollution events involving nitrate and sulphate, in combination with organic carbon. We then observed the microbiota composition the following month. Surprisingly, upon nitrate addition, an abrupt response was observed between two and three weeks after the pollution event. We observed a threefold reduction in species richness, with a dominance of the genus Pseudarchobacter within the Campylobacteriota phylum, concurring with a decrease in nitrification potential and an increase in Dissimilatory Nitrate Reduction to Ammonium (DNRA) and a regain in denitrification. Likewise, addition of sulphate contributed to a delayed response with reduction in species richness albeit weaker than for nitrate, leading to a shift towards potential spore-forming Firmicutes. There was also an increase in DNRA, but only for the oxic conditions, concurring with a regain in sulphate reductio and denitrification. For the nitrate addition experiments, the delay in response could potentially be attributed to the genus Pseudarchobacter which rely on sulphides for denitrification, while for the sulphate addition experiments, the delayed response might be explained by the germination of spores. The late increase of DNRA may indicate a shift towards a different metabolic regime for nitrogen. In conclusion, our microcosm experiments revealed delayed abrupt microbiota shifts resembling tipping points that can potentially be overlooked in natural ecosystems.

Perturbations to common gardens of anaerobic co-digesters reveal relationships between functional resilience and microbial community composition

We report the relationship between enrichment of adapted populations and enhancement of community functional resilience in methanogenic bioreactors. Although previous studies have shown the positive effects of acclimation, this work directly investigated the relationships between microbiome dynamics and performance of anaerobic co-digesting reactors in response to different levels of an environmental perturbation (loading of grease interceptor waste [GIW]). Using the methanogenic microbiome from a full-scale digester, we developed eight sets of microbial communities in triplicate using different feed sources. These substrate-specific microbiomes were then exposed to three independent disturbance events of low-, mid- and high-GIW loading rates. This approach allowed us to directly attribute differences in community responses to differences in community composition. Despite identical inocula, environment (digester operation, substrate loading rate, and feeding patterns) and general whole-community function (methane production and effluent quality) during the cultivation period, different substrates led to different microbial community assemblies. Lipid pre-acclimation led to enrichment of a pool of specialized populations, along with thriving of sub-dominant communities. The enrichment of these populations improved functional resilience and process performance when exposed to a low level of lipid-rich perturbation compared with less-acclimated communities. At higher levels of perturbation, the communities were not able to recover methanogenesis, indicating a loading limit to the resilience response. This study extends our current understanding of environmental perturbations, feed-specific adaptation, and functional resilience in methanogenic bioreactors.IMPORTANCEThis study demonstrates, for the first time for GIW co-digestion, how applying similar perturbations to different microbial communities was used to directly identify the causal relationships between microbial community, function, and environment in triplicate anaerobic microbiomes. We evaluated the impact of feed-specific adaptation on methanogenic microbiomes and demonstrated how microbiomes can be influenced to improve their functional (methanogenic) resilience to GIW inhibition. These findings demonstrate how an ecological framework can help improve a biological engineering application, and more specifically, increase the potential of anaerobic co-digestion for converting wastes to energy.

Linking microbial population dynamics in anaerobic bioreactors to food waste type and decomposition stage

A key question in anaerobic microbial ecology is how microbial communities develop over different stages of waste decomposition and whether these changes are specific to waste types. We destructively sampled over time 26 replicate bioreactors cultivated on fruit/vegetable waste (FVW) and meat waste (MW) based on pre-defined waste components and composition. To characterize community shifts, we examined 16S rRNA genes from both the leachate and solid fractions of the waste. Waste decomposition occurred faster in FVW than MW, as accumulation of ammonia in MW reactors led to inhibition of methanogenesis. We identified population succession during different stages of waste decomposition and linked specific populations to different waste types. Community analyses revealed underrepresentation of methanogens in the leachate fractions, emphasizing the importance of consistent and representative sampling when characterizing microbial communities in solid waste.

Effects of tomato straw fermentation on nutrients and bacterial community structure

Unsustainable straw treatment methods detrimentally affect the environment and ecology. Aerobic fermentation (AE) and anaerobic fermentation (AN) are environmentally friendly treatments that better utilise straw resources. In this study, high-throughput sequencing was used to investigate the effects of AE and AN on nutrient content and microbial community structure during tomato straw fermentation. Nitrate nitrogen, available phosphorus, available potassium, and fulvic acid contents following AE were 1250.04 mg/kg, 80.34 %, 161.39 %, and 49.31 %, respectively, which were higher than those following AN. Ammonium nitrogen, humic acid, and humic substance levels following AN were 309.07 %, 31.18 %, and 17.38 %, respectively, which were higher than those following AE. Firmicutes (24.76 %) and Actinobacteria (12.93 %) were more abundant following AE, whereas Proteobacteria (33.82 %) and Bacteroidetes (33.82 %) exhibited higher abundance following AN. AE more effectively eliminated pathogenic bacteria (22.01%-0.26 %) and encouraged stronger interactions between dominant bacterial genera. Redundancy and Mantel test analyses revealed that electrical conductivity and temperature were the most important environmental factors affecting bacterial communities in AE and AN, respectively. AE had a stronger effect on effective nutrient release from tomato straw, implying its greater application potential as a fertiliser. Overall, our study provides a theoretical basis for the optimisation of fermentation methods and processes.

Effects of fructan and gluten on gut microbiota in individuals with self-reported non-celiac gluten/wheat sensitivity-a randomised controlled crossover trial

BACKGROUND

Individuals with non-celiac gluten/wheat sensitivity (NCGWS) experience improvement in gastrointestinal symptoms following a gluten-free diet. Although previous results have indicated that fructo-oligosaccharides (FOS), a type of short-chain fructans, were more likely to induce symptoms than gluten in self-reported NCGWS patients, the underlying mechanisms are unresolved.

METHODS

Our main objective was therefore to investigate whether FOS-fructans and gluten affect the composition and diversity of the faecal microbiota (16S rRNA gene sequencing), faecal metabolites of microbial fermentation (short-chain fatty acids [SCFA]; gas chromatography with flame ionization detector), and a faecal biomarker of gut inflammation (neutrophil gelatinase-associated lipocalin, also known as lipocalin 2, NGAL/LCN2; ELISA). In the randomised double-blind placebo-controlled crossover study, 59 participants with self-reported NCGWS underwent three different 7-day diet challenges with gluten (5.7 g/day), FOS-fructans (2.1 g/day), and placebo separately (three periods, six challenge sequences).

RESULTS

The relative abundances of certain bacterial taxa were affected differently by the diet challenges. After the FOS-fructan challenge, Fusicatenibacter increased, while Eubacterium (E.) coprostanoligenes group, Anaerotruncus, and unknown Ruminococcaceae genera decreased. The gluten challenge was primarily characterized by increased abundance of Eubacterium xylanophilum group. However, no differences were found for bacterial diversity (α-diversity), overall bacterial community structure (β-diversity), faecal metabolites (SCFA), or NGAL/LCN2. Furthermore, gastrointestinal symptoms in response to FOS-fructans were generally not linked to substantial shifts in the gut bacterial community. However, the reduction in E. coprostanoligenes group following the FOS-fructan challenge was associated with increased gastrointestinal pain. Finally, correlation analysis revealed that changes in gastrointestinal symptoms following the FOS-fructan and gluten challenges were linked to varying bacterial abundances at baseline.

CONCLUSIONS

In conclusion, while FOS-fructans induced more gastrointestinal symptoms than gluten in the NCGWS patients, we did not find that substantial shifts in the composition nor function of the faecal microbiota could explain these differences in the current study. However, our results indicate that individual variations in baseline bacterial composition/function may influence the gastrointestinal symptom response to both FOS-fructans and gluten. Additionally, the change in E. coprostanoligenes group, which was associated with increased symptoms, implies that attention should be given to these bacteria in future trials investigating the impact of dietary treatments on gastrointestinal symptoms.

TRIAL REGISTRATION

Clinicaltrials.gov as NCT02464150.