Microbial Indicators Research Articles

Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary

Abstract Anthropogenic influences have drastically increased nutrient concentrations in many estuaries globally, and microbial communities have adapted to the resulting hypereutrophic ecosystems. However, our knowledge of the dominant microbial taxa and their potential functions in these ecosystems has remained sparse. Here, we study prokaryotic community dynamics in a temporal–spatial dataset, from a subtropical hypereutrophic estuary. Screening 54 water samples across brackish to marine sites revealed that nutrient concentrations and salinity best explained spatial community variations, whereas temperature and dissolved oxygen likely drive seasonal shifts. By combining short and long read sequencing data, we recovered 2,459 metagenome-assembled genomes, proposed new taxon names for previously uncharacterised lineages, and created an extensive, habitat specific genome reference database. Community profiling based on this genome reference database revealed a diverse prokaryotic community comprising 61 bacterial and 18 archaeal phyla, and resulted in an improved taxonomic resolution at lower ranks down to genus level. We found that the vast majority (61 out of 73) of abundant genera (>1% average) represented unnamed and novel lineages, and that all genera could be clearly separated into brackish and marine ecotypes with inferred habitat specific functions. Applying supervised machine learning and metabolic reconstruction, we identified several microbial indicator taxa responding directly or indirectly to elevated nitrate and total phosphorus concentrations. In conclusion, our analysis highlights the importance of improved taxonomic resolution, sheds light on the role of previously uncharacterised lineages in estuarine nutrient cycling, and identifies microbial indicators for nutrient levels crucial in estuary health assessments.

Development of a microbial time-temperature indicator for real-time monitoring the quality of Australian vacuum-packed lamb

A time-temperature indicator (TTI) system based on the pH-dependent colour change caused by the growth of a Carnobacterium maltaromaticum strain was developed to specifically provide a real-time indication of quality and shelf life of Australian vacuum-packed (VP) lamb throughout cold chains. Each component of the developed TTI system was studied to select an optimal concentration of a chemical chromatic indicator (chlorophenol red, CR; between 0.01 % and 0.30 %) and supplementary glucose (between 0 % and 10 %), and an appropriate C. maltaromaticum strain (among four different strains) in a simple BHI medium. BHI medium containing 0.01 % CR and 1 % added glucose, inoculated with C. maltaromaticum strain 1 were required for development of the TTI system to indicate quality and shelf life of VP lamb. Different inoculum levels of C. maltaromaticum strain 1 (103 to 105 CFU/mL) were also examined at 8 °C for their effects on the TTI response. As expected, higher inoculum levels of C. maltaromaticum led to a shorter endpoint of the TTI system but it was found that a 3 log10 higher inoculum level in the TTI than the expected total viable counts of VP lamb was required to accurately predict VP lamb shelf life by the TTI. To further evaluate the applicability of the TTI system, we evaluated its response at two other temperatures (2 °C and 4 °C) relevant to the storage conditions for VP lamb. The data showed a strong agreement between the observed TTI's endpoints and predicted shelf lives of VP lamb. This indicated that the developed TTI has the potential to be developed further for commercial application to provide a real-time, distinct, and accurate indication of Australian VP lamb.

An assessment of soil microbial community environmental stress in alpine marginal ecosystems using microbial indicators

Alpine marginal ecosystems above the natural tree line are considered to be the most vulnerable habitats for maintaining local biodiversity. The soil microbial community is crucial for ecosystem stability and function. However, our comprehension of the overall soil microbial community in alpine marginal ecosystems remains limited, particularly regarding environmental stress. We selected the Baima Mountain National Nature Reserve (BMNNR) in the northwest Yunnan provinces as our study area and collected soil samples from three different depth layers, in alpine marginal ecosystems. The phospholipid fatty acid (PLFA) analysis method was utilized to evaluate alterations in soil microbial communities. The results showed that: (1) the PLFA content gradually decreased with increasing soil depth; (2) on the whole, the variations in PLFA across alpine marginal ecosystems were obviously, the highest in alpine meadow (AM) and the lowest in alpine screes (AS); (3) the site effect exerted a greater direct influence than microhabitat effect and elevation (0–5 cm, 32 %, 16 % and 9 %, respectively; 20–40 cm, 46 %, 29 % and 0 %, respectively), with the direct impact of elevation decreasing as soil depth increased (0–5 cm, 5–20 cm and20-40 cm, 9 %, 1 % and 0 %, respectively); and (4) the ratio of cyclopropyl to precursors (Cy:Pre) in all communities was > 0.1, indicating that the soil microbial community was under environmental stress. This study demonstrates the potential of PLFA analysis to profile soil microbial communities and their stress status under field conditions and also provides a better understanding of the correlation between soil microbial communities and the function and health of alpine marginal ecosystems.

Genetic liability of gut microbiota for idiopathic pulmonary fibrosis and lung function: a two-sample Mendelian randomization study.

The microbiota-gut-lung axis has elucidated a potential association between gut microbiota and idiopathic pulmonary fibrosis (IPF). However, there is a paucity of population-level studies with providing robust evidence for establishing causality. This two-sample Mendelian randomization (MR) analysis aimed to investigate the causal relationship between the gut microbiota and IPF as well as lung function. Adhering to Mendel's principle of inheritance, this MR analysis utilized summary-level data from respective genome-wide association studies (GWAS) involving 211 gut microbial taxa, IPF, and lung function indicators such as FEV1, FVC, and FEV1/FVC. A bidirectional two-sample MR design was employed, utilizing multiple MR analysis methods, including inverse variance-weighted (IVW), weighted median, MR-Egger, and weighted mode. Multivariable MR (MVMR) was used to uncover mediating factors connecting the exposure and outcome. Additionally, comprehensive sensitivity analyses were conducted to ensure the robustness of the results. The MR results confirmed four taxa were found causally associated with the risk of IPF. Order Bifidobacteriales (OR=0.773, 95% CI: 0.610-0.979, p=0.033), Family Bifidobacteriaceae (OR=0.773, 95% CI: 0.610-0.979, p=0.033), and Genus RuminococcaceaeUCG009 (OR=0.793, 95% CI: 0.652-0.965, p=0.020) exerted protective effects on IPF, while Genus Coprococcus2 (OR=1.349, 95% CI: 1.021-1.783, p=0.035) promote the development of IPF. Several taxa were causally associated with lung function, with those in Class Deltaproteobacteria, Order Desulfovibrionales, Family Desulfovibrionaceae, Class Verrucomicrobiae, Order Verrucomicrobiales and Family Verrucomicrobiaceae being the most prominent beneficial microbiota, while those in Family Lachnospiraceae, Genus Oscillospira, and Genus Parasutterella were associated with impaired lung function. As for the reverse analysis, MR results confirmed the effects of FEV1 and FVC on the increased abundance of six taxa (Phylum Actinobacteria, Class Actinobacteria, Order Bifidobacteriales, Family Bifidobacteriaceae, Genus Bifidobacterium, and Genus Ruminiclostridium9) with a boosted level of evidence. MVMR suggested monounsaturated fatty acids, total fatty acids, saturated fatty acids, and ratio of omega-6 fatty acids to total fatty acids as potential mediating factors in the genetic association between gut microbiota and IPF. The current study suggested the casual effects of the specific gut microbes on the risk of IPF and lung function. In turn, lung function also exerted a positive role in some gut microbes. A reasonable dietary intake of lipid substances has a certain protective effect against the occurrence and progression of IPF. This study provides novel insights into the potential role of gut microbiota in IPF and indicates a possible gut microbiota-mediated mechanism for the prevention of IPF.

Changes in groundwater and surface water bacterial communities under disinfection processes: Chlorination, ozonization, photo-fenton and ultraviolet radiation

Pathogenic bacteria, introduced in water sources through faecal contamination, have traditionally been investigated as individual species, leading to the establishment of microbial, sanitary, and environmental quality indicators. Recent advancements in our understanding of the microbiome and its intricate interactions within the human-microbiome-environment network advocate for a broader evaluation of the impact of disinfection on the entire microbial community. In this study, we conducted a comprehensive screening experiment involving four disinfection processes; ozone, ultraviolet radiation with wavelengths between 200 – 280 nm (UV-C), photo-Fenton, and chlorination, applied to two distinct water sources; surface (SW) and groundwater (GW). The cells that remained viable after treatment were recovered using Brain Heart Infusion (BHI) broth, and 16S rRNA gene sequencing was used for their identification. Our findings confirmed the presence of faecal contamination in the water sources and revealed distinct effects of each treatment on the recovered bacterial populations. The chlorination of groundwater samples likely had a greater impact on bacteria in a vegetative state than on spores. Consequently, this led to a higher abundance in the BHI cultures of sporulating bacteria such as Bacillus (increasing from 0.36 to 93.62 %), while ozonation led to an elevated recovery of Pseudomonas (increasing from 45.2 to 69.9 %). Conversely, in surface water, calcium hypochlorite and ozone treatments favored the selection of Staphylococcus and Bacillus, whose relative abundance in the cultures increased from 0 to 39.22 % and from 0.35 to 96.6 %, respectively. In groundwater, Pseudomonas was resistant to UV-C radiation and their relative abundance increased from 45.2 % to 93.56 %, while photo-Fenton was effective against this bacterial group decreasing its relative abundance to 0.46 %. However, other genera such as Bacteroides, Aeromonas, and Citrobacter seemed to be less injured by this disinfection process. BHI broth was successful in recovering various bacterial groups that exhibited resistance to sublethal water disinfection.

Microbial eukaryote community succession over hundreds of years in Chinese lakes

Microbial eukaryotes play critical roles in maintaining the health and stability of lake ecosystems. Consequently, investigating the spatial and temporal evolution of microbial eukaryotic community structures and associated environmental drivers can inform water ecology studies and water environmental protection efforts. In this study, sediment core samples were collected from Lakes Chaohu, Erhai, Lugu and Fuxian in China to reconstruct lake microbial eukaryotic community succession using sediment DNA profiling methods. Mantel tests were used to identify the key factors influencing community succession and explore the mechanisms underlying ecological network changes. Statistical analyses revealed that community structures and diversity in Lakes Chaohu and Erhai shifted in the 2000s and 1980s, respectively, while the communities of Lakes Fuxian and Lugu did not exhibit significant changes during the study period, which may be due to the oligotrophic state of these two lakes. Ciliophora and Chlorophyta were the primary eukaryotic microbial taxa in the four lakes during the study period, with overall relative abundances of 27.2 % and 22.3 %, respectively. The diversities of microbial eukaryotic communities in the lakes were significantly correlated with nutrient enrichment and meteorological factors. Lastly, the ecological niche gap of microbial eukaryotes gradually overlapped after community shifts in Lake Chaohu, while biased interactions strengthened. Overall, this study reveals the impacts of long-term human activities and climate change on lake ecosystems from multiple perspectives of microbial eukaryotic community structure, diversity and ecological network, these findings will contribute to integrate microbial indicators in freshwater environmental monitoring in the future.

Coastal distribution and driving factors for blue carbon fractions in the surface soil of a warm-temperate salt marsh in China

A better understanding of blue carbon (BC) sequestration can not only contribute to a better elucidation of global carbon cycle processes but can also lay the foundation for the incorporation of BC ecosystems into regional and global carbon offset schemes. In this study, the surface soils of seven plots along a landward to seaward distance gradient were analyzed for the concentrations and stocks of soil organic carbon (SOC), soil inorganic carbon (SIC), dissolved organic carbon (DOC), and dissolved inorganic carbon (DIC), as well as soil physical (bulk density, texture, moisture), chemical (pH, electrical conductivity), and microbiological (phospholipid fatty acid) properties in the coastal wetlands. Correlation, variation partition and random forest (RF) analyses were used to identify key variables correlating with BC fraction distribution patterns. The results suggested that SIC, DIC, and DOC, exhibited similar landward-increasing trends but the driving factors were distinct from each other. Based on correlation and RF analysis, both SIC and DIC were closely related to soil moisture and clay contents, but microbial indicators of arbuscular mycorrhizal fungi and actinomycete, were found to be associated with SIC, and abiotic properties played less important but still substantial roles in predicting DIC dynamics. In contrast with the other three investigated BC fractions, SOC showed a slight tendency toward enrichment in the seaward direction, and SIC was identified as the main driving factor. DOC showed no significant correlations with the other BC fractions, and its variation could not be explained well by the selected edaphic parameters. The soils in the YRD's tidal Suaeda salsa salt marshes showed a significant negative coupled SOC–SIC correlation, which was potentially related to divergent sedimentary processes and potential biotransformation between SOC and SIC. These results highlight the importance of integrating multiple BC fractions and their interactions into attempts to explore key mechanisms of BC cycling.

Vostok Bay: interseasonal changes in hydrological, hydrochemical and microbiological properties

Current ecological state of the Vostok Bay (Peter the Great Bay, Japan Sea) in spring, summer, and autumn seasons is described on the data of CTD profiling, chemical analysis of the water sampled at the sea surface and bottom, and microbial indication of the surface water. Strong seasonal variations are revealed for all examined parameters, driven by monsoon cycle. The winter monsoon in autumn with northwestern wind predominance causes the river runoff weakening and off-shore surge with the water removal from the top of the bay and the compensating inflow along the eastern coast distinguished by heightened values of salinity and dissolved oxygen and low values of biochemical oxygen demand (BOD5 < 1 mg/L). The summer monsoon in spring and summer with southeastern winds increases the river runoff and simultaneously the inflow of fresh water from the open sea, so causes a sharp difference in the water properties between parts of the Vostok Bay. Bioproductivity increases in these seasons that is reflected in increasing of BOD5 (up to 2 mg/L and sometimes more) and organic phosphorus concentration (up to 50 μg/L and more). In July, when the river runoff is blocked in the northwestern sector of the bay by onshore surge, the maximum number of bacteria is recorded there (up to 105 CFU/mL), including Escherichia coli group at all coastal stations in concentrations of 10–100 CFU/mL, which are not observed in the central and open parts of the bay. Among the groups of metal-resistant microorganisms, relative abundance of nickel-resistant bacteria is noted (up to 103 CFU/mL) that is a sign of hydrocarbon fuels combustion. The hydrocarbon pollution is confirmed by ubiquitous distribution of oil-oxidizing and diesel-resistant microorganisms detected mostly (up to 2.8 ∙ 104 CFU/mL in summer) in the northern part of the bay. Generally, the internal northern part of the bay is distinguished by high abundance of microorganisms belonged to different ecological and trophic groups, because of mutual impacts of the rivers, the coastal highway, nearby settlements, and sandy beaches occupied by vacationers in summer.

Molecular responses of sponge larvae exposed to partially weathered condensate oil

Anthropogenic inputs of petroleum hydrocarbons into the marine environment can have long lasting impacts on benthic communities. Sponges form an abundant and diverse component of benthic habitats, contributing a variety of important functional roles; however, their responses to petroleum hydrocarbons are largely unknown. This study combined a traditional ecotoxicological experimental design and endpoint with global gene expression profiling and microbial indicator species analysis to examine the effects of a water accommodated fraction (WAF) of condensate oil on a common Indo-Pacific sponge, Phyllospongia foliascens. A no significant effect concentration (N(S)EC) of 2.1 % WAF was obtained for larval settlement, while gene-specific (N(S)EC) thresholds ranged from 3.4 % to 8.8 % WAF. Significant shifts in global gene expression were identified at WAF treatments ≥20 %, with larvae exposed to 100 % WAF most responsive. Results from this study provide an example on the incorporation of non-conventional molecular and microbiological responses into ecotoxicological studies on petroleum hydrocarbons.

Biological remediation treatments improve the health of a mixed contaminated soil before significantly reducing contaminant levels.

The remediation of mixed contaminated soil is challenging as it often requires actions to minimize metal-induced risks while degrading organic contaminants. Here, the effectiveness of different bioremediation strategies, namely, rhizoremediation with native plant species, mycoremediation with Pleurotus ostreatus spent mushroom substrate, and biostimulation with organic by-products (i.e., composted sewage sludge and spent mushroom substrate), for the recovery of a mixed contaminated soil from an abandoned gravel pit was studied. The combination of biostimulation and rhizoremediation led to the most significant increase in soil health, according to microbial indicator values. The application of composted sewage sludge led to the highest reduction in anthracene and polychlorinated biphenyls concentrations. None of the strategies managed to decrease contamination levels below regulatory limits, but they did enhance soil health. It was concluded that the biological remediation treatments improved soil functioning in a short time, before the concentration of soil contaminants was significantly reduced.

Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments.

Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.

Identification of methane cycling pathways in Quaternary alluvial-lacustrine aquifers using multiple isotope and microbial indicators

Groundwater rich in dissolved methane is often overlooked in the global or regional carbon cycle. Considering the knowledge gap in understanding the biogeochemical behavior of methane in shallow aquifers, particularly those in humid alluvial-lacustrine plains with high organic carbon content, we investigated methane sources and cycling pathways in groundwater systems at the central Yangtze River basins. Composition of multiple stable isotopes (2H/18O in water, 13C in dissolved inorganic carbon, 13C/2H in methane, and 13C in carbon dioxide) was combined with the characteristics of microbes and dissolved organic matter (DOM) in the study. The results revealed significant concentrations of biogenic methane reaching up to 13.05 mg/L in anaerobic groundwater environments with abundant organic matter. Different pathways for methane cycling (methanogenic CO2-reduction and acetate-fermentation, and methane oxidation) were identified. CO2-reduction dominated acetate-fermentation in the two methanogenic pathways primarily associated with humic DOM, while methane oxidation was more closely associated with microbially derived DOM. The abundance of obligate CO2-reduction microorganisms (Methanobacterium and Methanoregula) was higher in samples with substantial CO2-reduction, as indicated by isotopic composition. The obligate acetate-fermentation microorganism (Methanosaeta) was more abundant in samples exhibiting evident acetate-fermentation. Additionally, a high abundance of Candidatus Methanoperedens was identified in samples with apparent methane oxidation. Comparing our findings with those in other areas, we found that various factors, such as groundwater temperature, DOM abundance and types, and hydrogeological conditions, may lead to differences in groundwater methane cycling. This study offered a new perspective and understanding of methane cycling in worldwide shallow alluvial-lacustrine aquifer systems without geothermal disturbance.

Fungal community composition changes and reduced bacterial diversity drive improvements in the soil quality index during arable land restoration

Arable land is facing the growing challenge of land degradation due to intensive use and this is beginning to affect global food security. However, active and passive restoration can improve soil characteristics and reshape microbial communities. Despite the increasing focus on changes in microbial communities during restoration, the mechanisms underlying how microbes drive the soil quality index (SQI) in arable land restoration remain unclear. In this study, we selected conventional farmland (CF, heavily intensified) and two restoration strategies (AR, artificial restoration; NR, natural restoration), with the same context (including soil texture, climate, etc.), and measured the microbial indicators over 2 years to investigate the mechanisms driving SQI improvement on restored arable land. The AR and NR treatments resulted in a 50% and 58% increase in SQI, respectively, compared to CF as soil nutrient levels increased, resulting in higher microbial biomasses and enzyme activities. Microbial abundance on the AR land was approximately two times greater than on the NR land due to the introduction of legumes. Bacterial diversity declined, while fungi developed in a more diverse direction under the restoration strategies. The AR and NR areas were mainly enriched with rhizobium (Microvirga, Bradyrhizobium), which contribute to healthy plant growth. The pathogenic fungi (Gibberella, Fusarium, Volutella) were more abundant in the CF area and the plant pathogen guild was about five times higher in the restored areas. Following arable land restoration, microbial life history strategies shifted from r-to K-strategists due to the higher proportion of recalcitrant SOC (DOC/SOC decreased by 18%–30%). The altered microbial community in the restored areas created new levels of functionality, with a 2.6%–4.3% decrease in bacterial energy metabolism (oxidative phosphorylation, C fixation, and N metabolism decreased by 7%, 4%, and 6%, respectively). Structural equation modelling suggested that restoration strategy affected SQI either directly by increasing total soil nutrient levels or indirectly by altering the microbial community and that fungal community composition and bacterial diversity made the largest contributions to SQI. These results provided new insights into soil quality improvement from a microbial perspective and can help guide future arable land restoration.

Somatic Coliphages as an Operational Tool to Assess Loss of Bathing Water Quality after Heavy Rain Events

Rapid population growth and coastal development has led to increased fecal contamination of coastal surface waters worldwide, enhancing the potential risk of waterborne human pathogens in bathing areas. More frequent heavy rainfall events, attributed to global warming, have further exacerbated the problem by causing sometimes sewer overflows into recreational waters. As traditional bacterial indicators have limited accuracy for predicting health risks associated with waterborne viruses, the additional use of viral indicators such as coliphages is recommended. In this study, we compared the behavior of bacterial and viral indicators of water quality at 10 Barcelona beaches during three bathing seasons, in dry conditions, and after four rainstorms that caused specific pollution events due to rain runoff with combined sewer overflows (CSO). Levels of all target indicators increased after the rainstorms, but compared to Escherichia coli and intestinal enterococci, somatic coliphages exhibited a slower decline and higher environmental persistence following a rain event. Daily continuous sampling carried out during the days following a rainstorm allowed not only the determination of the decay kinetics of each target indicator but also the day when the water quality recovered the values established in the current European regulation in approximately 2 -3 days after each CSO. These observations indicate that the combined use of bacterial and viral indicators can enhance the surveillance of microbial quality of bathing waters. Moreover, coliphages can swiftly provide insights into transient fecal pollution linked to rainfall episodes, thanks to available analytical techniques that enable same-day recommendations. The management of urban wastewater and recreational water regulations should consistently employ microbial indicators to address rainwater runoff or sewer overflows resulting from heavy rainfall.

Temperature and moisture sensitivities of soil respiration vary along elevation gradients: An analysis from long-term field observations

Based on long-term field observation data over 11 years at 23 sites in two mountainous areas (TS1 and TS2) at elevations from 829 to 2700 m, where the dominant vegetation type of TS1 and TS2 was temperate mixed broadleaf-coniferous forest and cold temperate coniferous forest, respectively, we analyzed the correlations between soil respiration (Rs) and abiotic and biotic factors to explore the response patterns of Rs to environmental factors within and between the sites along the elevation gradient. We found that soil moisture (θ) and its combinations (Ts × θ and θ/Ts) with soil temperature (Ts) increased significantly with increasing elevation, while Ts, soil bulk density (SBD), C/N ratio, and pH decreased significantly with increasing elevation. Within each site, both exponential- Ts (ET) and Gaussian-Ts (GT) models could be used for predicting the Rs seasonal variation, except for two sites in the area of TS1, where θ was a better predictor than Ts. The integrated ET–θ and GT–θ models could be applied to all sites except for 22S, and both were superior to the ET and GT models. The mean Rs of each site over the measurement period ranged from 3.07 to 6.94 μmol CO2 m−2 s−1 and showed a quadratic increase along the elevation gradient. Among the 23 sites, Q10 ranged from 1.15 to 3.79, and it increased with elevation, reaching a maximum at an elevation of 2366 m; the θ sensitivity parameter (d) decreased significantly with elevation and reached a minimum at an elevation of 1975 m. Both the d and Ts sensitivity parameter (b) of Rs were complementary to each other along the elevation gradient. Among the sites, Ts, θ, and combinations of the two were more important drivers for both Rs and Q10 variations than microbial and physicochemical indicators.

Seasonal Comparison of Microbial Hygiene Indicators in Raw and Pasteurized Milk and Cottage Cheese Collected across Dairy Value Chain in Three Regions of Ethiopia.

A longitudinal design with a simple random sampling method was used to collect and compare microbial hygiene levels between the dry season (January to April) and wet season (June to August). A total of 456 milk and cottage cheese samples were collected from each site along the dairy value chain from three regions. Enumeration of total aerobic mesophilic bacteria (APC), total coliforms (TCC), and Escherichia coli (EC) was performed according to standard methods. Independent t-tests were employed to assess the significant variation at (p < 0.05) between the two seasons. The cumulative result of APC of 7.61 log cfu/mL and g and TCC of 3.50 log cfu/mL in the dry season were significantly higher than the wet season of 7.15 log cfu/mL and 2.49 log cfu/mL, respectively, whereas generic E. coli count (EC) was significantly higher in the wet season (0.70 log cfu/mL and g) than that in the dry season (0.40 log cfu/mL and g). The results of hygienic indicator microbial load significantly varied with season. Hence, hygienic milk production and handling practices that comprehend seasonal influence should be implemented to improve the safety of milk.

Effects of Afforestation Patterns on Soil Nutrient and Microbial Community Diversity in Rocky Desertification Areas

Karst ecosystems are characterized by the dissolution of soluble rocks, displaying distinctive landscape features such as rugged peaks, steep slopes, and deep valleys. Afforestation is an effective approach for improving soil quality in rocky desertification areas because plants have evolved unique adaptations to thrive in such environments. However, the effects of tree species composition and cultivation patterns on the soil quality, microbial diversity, stability, and functions in rocky desertification areas remain unclear. In this work, four study plots including three types of forests—pure Pinus massoniana plantations, Toona sinensis plantations, mixed coniferous and broadleaf plantations (Pinus massoniana–Betula luminifera forests), and unforested area as the control—were established in a karst desertification area in the Hunan province of China. Soil properties including soil bulk density, soil organic carbon, total nitrogen, total phosphate, soil ammonium nitrogen, nitrate, available phosphate, soil pH, and soil microbial diversity were investigated in the study area. The results showed that the forests significantly increased the soil organic carbon, total nitrogen, and ammonium nitrogen compared to the unforested area. The microbial diversity indicators in mixed forests were significantly higher than those in the Pinus massoniana forests. The dominant bacteria phyla included Proteobacteria, Acidobacteria, and Actinobacteria, while fungi species such as Ascomycota and Basidiomycota were identified in all study plots. In addition, the AVD index evaluation revealed that the mixed forests enhanced the stability of the soil microbial communities compared to the monoculture plantations and unforested plots in rocky desertification areas. The research results indicated that, among the various forest types, the mixed forest was the most effective choice for afforestation in terms of improving the soil quality by changing the soil’s physiological properties in rocky desertification areas. Our study provided guidance and insights for afforestation technology and the optimal allocation of different tree species in the cultivation and management of plantation forests in rocky desertification regions.

Effect of Individual and Synergistic Addition of Moringa Oliveira Seeds and Leaves Powder to Broiler Diets in some Physiological and Microbial Traits and Oxidation Indicators

This study was conducted at the poultry farm\\Abu Ghraib, College of Agricultural Engineering Sciences, University of Baghdad, for the period from 12-10-2022 to 22-11-2022 for 42 days to study the effect of individual and synergistic addition of Moringa oleifera seeds and leaves powder to broiler diets on some physiological and microbial traits. 210 commercial broiler chicks (Ross-308) one day old unsexed, randomly distributed to seven treatments with three replicates 10 birds each replicate and the treatments were contained: T1 (control treatment) without additive, T2: 1% seeds powder, T3: 2% seeds powder, T4: 1% leaves powder, T5: 2% leaves powder, T6: 0.5% seeds powder + 0.5 leaves powder, T7: 1% seeds powder + 1% leaves powder. The results indicated that no significant differences appeared between all the parameters in the biochemical characteristics of blood lipids, while the addition treatments recorded a significant decrease (P≤0.05) in the value of peroxide (P.V) and in the value of malondialdehyde (MDA) and free fatty acids (FFA) in the liver compared to the control treatment. As well as a significant increase (P≤0.05) was observed for the numbers of beneficial bacteria for the T5 bird group compared to the control treatment, T5 recorded a significant decrease (P≤0.05) in the numbers of harmful bacteria compared to the control treatment. It can be concluded that adding individually and synergistically Moringa oleifera seeds and leaves powder to broiler diets improves some of the immune and microbial traits.

Evaluating the Major Sources of Surface Water Quality in Pokhara Metropolitan City, Gandaki Province, Nepal

The Mardi Watershed serves as a crucial source of drinking water for Pokhara Metropolitan City (PMC), Gandaki Province, Nepal, offering a wide range of ecosystem services including fishing, tourism, transportation, livestock support, and, notably, clean drinking water. However, the main river and its tributaries face degradation due to a blend of human and natural impacts. This comprehensive study rigorously examines the physicochemical and biological attributes that define water quality within the watershed. Recognizing the global importance of water quality for human well-being, this investigation specifically evaluates the suitability of water for drinking purposes. Twenty-three samples were collected and subjected to analysis for the twenty-one distinct physicochemical parameters. The analysis covers physicochemical parameters such as pH, water temperature, conductivity, total dissolved solids, alkalinity as well as concentrations of ions such as calcium (Ca2+), magnesium (Mg2+), sodium (Na+), potassium (K+), ammonium (NH4+), nitrate (NO3-), bicarbonate (HCO3-), sulfate (SO42-), and phosphate (PO43-), free carbon dioxide (CO2), chloride (Cl-), total hardness (TH), calcium hardness (CaH), magnesium hardness (MgH), iron (Fe2+), turbidity (Turb.) Simultaneously, biological markers including total coliforms were assessed. The overall water quality aligns with the World Health Organization (WHO) guidelines, a significant exception lies in microbial indicators. Microbial presence, likely a result of increasing anthropogenic pressures, is relatively elevated in most samples. Furthermore, the cumulative outcome reveals a Water Quality Index (WQI) of 22.04, indicating excellent suitability for drinking. Since, effective management strategies are crucial for ensuring a consistent and sustainable supply of potable water to the urban population, information obtained through this study can contribute to the sustainable management of water quality and maintaining a reliable supply of safe drinking water to urban communities.

Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota

Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments.