Changes In Microbial Composition Research Articles

Temperature and organic carbon quality control the anaerobic carbon mineralization in peat profiles via modulating microbes: A case study of Changbai Mountain

Peatlands account for a significant fraction of the global carbon stock. However, the complex interplay of abiotic and biotic factors governing anaerobic carbon mineralization in response to warming remains unclear. In this study, peat sediments were collected from a typical northern peatland-Changbai Mountain to investigate the behavior and mechanism of anaerobic carbon mineralization in response to depth (0–200 cm) and temperature (5 °C, 15 °C and 20 °C), by integrating geochemical and microbial analysis. Several indices including humification indexes (HI), aromaticity, and water extractable organic carbon (WEOC) components were applied to evaluate carbon quality, while 16S rRNA sequencing was used to measure microbial composition. Regardless of temperature, degradations of carbon quality and associated reduction in microbial abundance as well as diversity resulted in a decrease in anaerobic carbon mineralization (both CO2 and CH4) towards greater depth. Warming either from 5 °C to 15 °C or 20 °C significantly increased anaerobic carbon mineralization in all depth profiles by improving carbon availability. Enhanced carbon availabilities were mediated by the change in microbial composition (p < 0.01) and an increase in metabolic activities, which was particularly evident in the enhanced β-glucosidase activity and microbial collaborations. A remarkable increase of over 10-fold in the relative abundance of the Geothrix genus was observed under warming. Overall, warming resulted in an enhanced contribution of CH4 emission and a higher ratio of hydrogenotrophic methanogenesis, as evidenced by carbon isotope fractionation factors. In addition, deep peat soils (>100 cm) with recalcitrant carbon demonstrated greater temperature sensitivity (Q10: ∼2.0) than shallow peat soils (Q10:∼1.2) when temperature increased from 15 °C to 20 °C. The findings of this study have significantly deepened our understanding for mechanisms of carbon quality and microbe-driven anaerobic carbon mineralization in peatlands under global warming.

Microbial and immune faecal determinants in infants hospitalized with COVID-19 reflect bifidobacterial dysbiosis and immature intestinal immunity

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly worldwide, seriously endangering human health. Although SARS‐CoV‐2 had a lower impact on paediatric population, children with COVID-19 have been reported as suffering from gastrointestinal (GI) symptoms at a higher rate than adults. The aim of this work was to evaluate faeces as a source of potential biomarkers of severity in the paediatric population, with an emphasis on intestinal microbiota and faecal immune mediators, trying to identify possible dysbiosis and immune intestinal dysfunction associated with the risk of hospitalization. This study involved 19 patients with COVID-19 under 24 months of age hospitalized during the pandemic at 6 different hospitals in Spain, and it included a comparable age-matched healthy control group (n = 18). Patients and controls were stratified according to their age in two groups: newborns or young infants (from 0 to 3 months old) and toddlers (infants from 6 to 24 months old). To characterize microbial intestinal communities, sequencing with Illumina technology of total 16S rDNA amplicons and internal transcribed spacer (ITS) amplicons of bifidobacteria were used. Faecal calprotectin (FC) and a range of human cytokines, chemokines, and growth factors were measured in faecal samples using ELISA and a multiplex system. Significant reduction in the abundance of sequences belonging to the phylum Actinobacteria was found in those infants with COVID-19, as well as in the Bifidobacteriaceae family. A different pattern of bifidobacteria was observed in patients, mainly represented by lower percentages of Bifidobacterium breve, as compared with controls. In the group of hospitalized young infants, FC was almost absent compared to age-matched healthy controls. A lower prevalence in faecal excretion of immune factors in these infected patients was also observed.Conclusion: Hospitalized infants with COVID-19 were depleted in some gut bacteria, such as bifidobacteria, in particular Bifidobacterium breve, which is crucial for the proper establishment of a functional intestinal microbiota, and important for the development of a competent immune system. Our results point to a possible immature immune system at intestine level in young infants infected by SARS-CoV2 requiring hospitalization.What is Known:• Although SARS‐CoV‐2 had a lower impact on paediatric population, children with COVID-19 have been reported as suffering from gastrointestinal symptoms at a higher rate than adults.• Changes in microbial composition have been described in COVID-19 adult patients, although studies in children are limited.What is New:• The first evidence that hospitalized infants with COVID-19 during the pandemic had a depletion in bifidobacteria, particularly in Bifidobacterium breve, beneficial gut bacteria in infancy that are crucial for the proper establishment of a competent immune system.• In young infants (under 3 months of age) hospitalized with SARS-CoV2 infection, the aberrant bifidobacterial profile appears to overlap with a poor intestinal immune development as seen by calprotectin and the trend of immunological factors excreted in faeces.

Remediation Effect and Mechanism of Biochar in Combination with Nitrogen Fertilizer on Cd-contaminated Paddy Soil

Cadmium (Cd) heavy metal pollution has posed serious threats to soil health and the safe production utilization of agricultural products. A pot experiment was conducted to study the effects of biochar (BC) and nitrogen fertilizer with three levels, namely 2.6 g·pot-1 (N1), 3.5 g·pot-1 (N2), 4.4 g·pot-1 (N3) biochar combined with nitrogen fertilizer (BCN1, BCN2, and BCN3), on soil Cd fractions, Cd enrichment, the transport of rice, and soil enzyme activity, as well as the changes in microbial community composition and complex interactions between microorganisms through high-throughput sequencing. The results showed that biochar combined with nitrogen fertilizer led to the transformation of Cd from the exchangeable state to the residue state, and the proportion of the exchangeable state was significantly reduced by 6.2%-14.7%; by contrast, the proportion of the residue state increased by 18.6%-26.4% relative to that in CK. In addition, singular treatments of nitrogen fertilizer enhanced the accumulation capacities of Cd in roots, which increased by 22%-33.5% compared with that in CK. By contrast, the BC and BCN treatments reduced Cd accumulation in roots and the transfer capacity from stems to rice husks and husk to rice. Furthermore, the BCN treatments promoted soil enzyme activities (urease, acid phosphatase, invertase, and catalase). MiSeq sequencing showed that BCN treatments increased the abundance of the main species of soil bacterial microbes (such as Acidobacteriales, Solibacterales, Pedosphaerales, and Nitrospirales). Moreover, co-occurrence network analysis showed that the complexity of the soil bacterial network was enhanced under the N, BC, and BCN treatments. Overall, biochar combined with nitrogen fertilizer reduced soil Cd availability, inhibited the capacity of Cd accumulation and the transport of rice, and improved the soil eco-environmental quality. Thus, using BCN could be a feasible practice for the remediation of Cd-polluted agricultural soil.

Succession of bacterial community structure in response to a one-time application of biochar in barley rhizosphere and bulk soils

Biochar is often used as an amendment to enhance soil fertility by directly increasing soil pH and nutrient availability. However, biochar may also improve soil fertility indirectly by altering the succession of bacterial communities that, in turn, may alter nutrient supply and availability. To determine how biochar affects soil bacterial richness and diversity, as well as how bacterial communities respond to biochar across space and time, we studied the rhizosphere and bulk soils of potted barley plants for 2 years. Adding biochar significantly increased bacterial community richness (Chao 1 richness index) by the end of the second year in the rhizosphere (P = 0.037), but in bulk soils, we observed an increase in richness in Year 1 that dissipated by Year 2. In contrast to richness, adding biochar only had a significant effect on bacterial community diversity (Shannon diversity index) in Year 1 seedling stage (P &amp;lt; 0.001), but the effect dissipated thereafter. We also found that adding biochar increased the relative abundances of Actinobacteria and Proteobacteria but decreased the relative abundances of Acidobacteria and Chloroflexi, suggesting these communities were sensitive to biochar inputs. The biochar-sensitive genera belonging to Actinobacteria and Proteobacteria made up 45%–58% of sensitive taxa in both rhizosphere and bulk soils. Of the Proteobacteria sensitive to adding biochar, Nitrosospira and Sphingomonas were most abundant in the rhizosphere relative to bulk soils. However, despite the initial increase of biochar sensitive responders in the rhizosphere, their numbers decreased after 2 years and had 179 fewer genera than bulk soils. Our findings suggest the effect of adding biochar was relatively short-lived and that the influence of the plant phenology was a stronger driver of bacterial community change than biochar inputs 2 years after its application. Altogether, the succession of soil bacterial community structure reflected changes in the soil environment induced by the combined effect of biochar, rhizospheric inputs, and plant phenology, suggesting that changes in microbial community composition observed after amending soils with biochar, may also contribute to changes in soil fertility.

Microbial composition and diversity of the tobacco leaf phyllosphere during plant development.

Phyllosphere-associated microorganisms affect host plant's nutrients availability, its growth and ecological functions. Tobacco leaves provide a wide-area habitat for microbial life. Previous studies have mainly focused on phyllosphere microbiota at one time point of tobacco growth process, but more is unknown about dynamic changes in phyllospheric microbial composition from earlier to the late stage of plant development. In the current study, we had determined the bacterial and fungal communities succession of tobacco growth stages (i.e., seedling, squaring, and maturing) by using both 16S rRNA sequencing for bacterial and ITS sequencing for fungi. Our results demonstrated that among tobacco growth stages, the phyllospheric bacterial communities went through more distinct succession than the fungal communities did. Proteobacteria and Actinobacteria exerted the most influence in tobacco development from seedling to squaring stages. At maturing stage, Proteobacteria and Actinobacteria dominance was gradually replaced by Firmicutes and Bacteroidetes. Network analysis revealed that Proteobacteria, as the core phyllospheric microbia, played essential role in stabilizing the whole bacterial network during tobacco development, and consequently rendered it to more profound ecological functions. During tobacco development, the contents of leaf sugar, nicotine, nitrogen and potassium were significantly correlated with either bacterial or fungal communities, and these abiotic factors accounted for 39.3 and 51.5% of the total variation, respectively. We overall evinced that the development of tobacco phyllosphere is accompanied by variant dynamics of phyllospheric microbial community.

A decade of microbial community dynamics on sinking particles during high carbon export events in the eastern Fram Strait

Marine sinking particles sequester atmospheric carbon dioxide to the deep ocean via the biological carbon pump. Understanding how environmental shifts drive changes in the microbial composition of particles, and how these affect the export of organic matter from the surface to the deep ocean, is critical, especially in the rapidly changing Arctic Ocean. Here, we applied next generation sequencing of the 18S and 16S rRNA genes to sediment trap samples from around 200 m water depth in the eastern Fram Strait, covering a time frame of more than one decade (2000-2012). The aim was to characterize their microbial composition during annual highest particulate organic carbon flux events. The bimodal annual spring and summer export fluxes were representative of the strong seasonality in the region. Furthermore, the study period was characterized by considerable interannual variation, marked especially by a warm water anomaly between 2005 and 2007. During this period changes in the hydrography and sea ice cover also led to measurable changes in the microbial composition of particles. The warm water period was marked by a decrease in diatoms affiliated with Chaetoceros, an increase of small phytoplankton and an increase in sequence abundance of the bacterial taxa Oceanospirillales, Alteromonadales and Rhodobacterales on the particles. The resulting changes in microbial composition and the associated microbial network structure suggest the emergence of a more developed retention system in the surface ocean. Our results provide the first long-term assessment of the microbial composition of sinking particles in the Arctic Ocean, and stress the importance of sea ice and hydrography for particle composition and subsequent flux of organic matter to deeper waters.

Influence of Gallic Acid-Containing Mouth Spray on Dental Health and Oral Microbiota of Healthy Dogs: A Pilot Study.

The pilot study aimed to investigate the effects of GAMS on oral microbiota in healthy dog subjects. Thirty-eight dogs were recruited and randomly allocated to the placebo (n = 19) and treatment groups (n = 19). The dogs were treated with mouth spray once daily for 42 days. The changes in the gingival index (GI), plaque index (PI), and calculus index (CI) were measured at baseline (day 0) and end of the study (42nd day). The changes in the oral microbial composition of representative dogs (placebo, n = 7; and treatment, n = 7) were also evaluated at baseline and end of the study. Oral microbial composition was assessed by sequencing. The sequences were annotated using the QIIME 2.0TM. The GI, PI, and CI indexes were reduced after the GAMS usage. The abundance of the commensal bacterial phylum Actinobacteria and Chloroflexi, genera Frederiksenia, and Bergeyella was improved after six weeks of GAMS usage. GAMS reduced the pathogenic bacterial species, including Neisseria sp., Desulfobulbus sp., Capnocytophaga canis, and Corynebacterium mustelae. Moreover, some pathogenic bacterial abundances were increased at the end of the study. All the microbial variations were observed within the group. The inter-group analysis revealed that the changes were unrelated to GAMS usage. Further studies need to be carried out using more experimental subjects to confirm the effectiveness of GAMS. More metagenomic data are required to evidence the GMAS impact on the oral microbiome of healthy dogs.

The Effect of Commonly Used Organic Acids on the Microbiota of Cured Deli-Style Turkey Breast

The purpose of this study was to investigate changes in the microbial community structure consisting of spoilage lactic acid bacteria (LAB) when sodium lactate (SL) and SL + sodium diacetate (SD) are included in RTE meat product formulations at concentrations commonly used for controlling Listeria monocytogenes. Sliced cooked, vacuum-packaged turkey breast samples containing no SD or SL (control [C]), 0.125% SD, and the combination of 2.5% SL + 0.125%SD (SLSD) were inoculated with a target of 3 log colony-forming units (CFU)/g of 5 different LAB species (Lactobacillus sakei, Leuconostoc mesenteroides [bacon and deli-shaved ham isolates], Lactococcus lactis, and Enterococcus faecium) and stored at 4°C for 35 d. Microbial community changes were analyzed utilizing 16S ribosomal RNA (rRNA) gene sequencing for the V4 region from the samples collected at days 0, 7, 14, 21, and 35. No significant difference (P&amp;gt;0.05) was observed between the richness of microbial community for all treatments. According to Bray-Curtis dissimilarity matrix and permutational analysis of variance, a significant difference in β-diversity was observed only between C and SLSD (P&amp;lt;0.05) because of the antimicrobial effect of the addition of SL that slowed down changes in microbial community composition until day 14. L. sakei remained a dominant strain throughout 35 d of storage regardless of treatment, whereas L. mesenteroides existed with a very low abundance. Two of the five strains were not seen after day 7. No significant effect (P&amp;gt;0.05) was observed for the SD treatment compared with C in the microbiota. According to the results from this study, only SLSD affected the microbial community structure at the beginning of the storage. This study demonstrated that the incorporation of SL in the formulation slowed down the microbial spoilage and the changes in the microbiota of RTE meat products.

Pleiotropic activities of succinate: The interplay between gut microbiota and cardiovascular diseases.

Cardiovascular diseases (CVDs) continue to be a significant contributor to global mortality, imposing a substantial burden and emphasizing the urgent need for disease control to save lives and prevent disability. With advancements in technology and scientific research, novel mechanisms underlying CVDs have been uncovered, leading to the exploration of promising treatment targets aimed at reducing the global burden of the disease. One of the most intriguing findings is the relationship between CVDs and gut microbiota, challenging the traditional understanding of CVDs mechanisms and introducing the concept of the gut-heart axis. The gut microbiota, through changes in microbial compositions and functions, plays a crucial role in influencing local and systemic effects on host physiology and disease development, with its metabolites acting as key regulators. In previous studies, we have emphasized the importance of specific metabolites such as betaine, putrescine, trimethylamine oxide, and N,N,N-trimethyl-5-aminovaleric acid in the potential treatment of CVDs. Particularly noteworthy is the gut microbiota-associated metabolite succinate, which has garnered significant attention due to its involvement in various pathophysiological pathways closely related to CVDs pathogenesis, including immunoinflammatory responses, oxidative stress, and energy metabolism. Furthermore, we have identified succinate as a potential biomarker, highlighting its therapeutic feasibility in managing aortic dissection and aneurysm. This review aims to comprehensively outline the characteristics of succinate, including its biosynthetic process, summarize the current evidence linking it to CVDs causation, and emphasize the host-microbial crosstalk involved in modulating CVDs. The insights presented here offer a novel paradigm for future management and control of CVDs.

Synthesis and evaluation of metal-impregnated carbon cloth supplementation to improve anaerobic digestion performance from municipal sludge

This study investigated the effect of metal-impregnated carbon cloth (CC) supplementation on thermophilic anaerobic digestion (AD) improvement by utilizing municipal sludge as a biomass input. Four types of metal-impregnated CC nanocomposites (Fe/CC, Ni/CC, Ni/Fe/CC, NiPcS/Fe/CC) were synthesized from activated CC (A-CC) using hydrothermal synthesis and compared with untreated CC (U-CC) to evaluate their functional significance for enhanced AD. The main factors inspected were electrical conductivity (EC) and Brunauer–Emmett–Teller (BET) surface area. A-CC had the highest surface area of 386.15 m2/g, followed by Fe/CC, NiPcS/Fe/CC, Ni/CC and Ni/Fe/CC with 140.96, 52.27, 43.52 and 36.07 m2/g, respectively. The A-CC and Fe/CC reactors produced 3.45 and 2.70 times more methane than Control (without CC) in the first 9 days. In contrast, the methane production for U-CC, Ni/CC, Ni/Fe/CC and NiPcS/Fe/CC was only 0.87, 1.26, 1.01 and 1.29 times, respectively, compared to Control. At a higher BET surface (>350 m2/g), the surface area becomes a more dominant factor, and the increase of EC value (>2.9*104 1/Ω.m) does not have an impact on methane enhancement. Microbial community analysis revealed that A-CC had the highest abundances of Syntrophomonas, Coprothermobacter and methanogenic populations, including Methanothermobacter and Methanosarcina, within 3 days compared to Control and metal-impregnated CC. There were minimal changes in microbial community composition in metal-impregnated CC compared to the U-CC. The result implies that the efficacy of CC supplementation for AD upgrading largely depends on the higher surface area compared to metal impregnation or conductivity.

Chronic Heat Stress Affects Bile Acid Profile and Gut Microbiota in Broilers.

Heat stress (HS) can inhibit the growth performance of broilers and cause substantial economic losses. Alterations in bile acid (BA) pools have been reported to be correlated with chronic HS, yet the specific mechanism and whether it is related to gut microbiota remains unclear. In this study, 40 Rugao Yellow chickens were randomly selected and distributed into two groups (20 broilers in each group) when reaching 56-day age: a chronic heat stress group (HS, 36 ± 1 °C for 8 h per day in the first 7 days and 36 ± 1 °C for 24 h in the last 7 days) and a control group (CN, 24 ± 1 °C for 24 h within 14 days). Compared with the CN group, total BAs' serum content decreased, while cholic acid (CA), chenodeoxycholic acid (CDCA), and taurolithocholic acid (TLCA) increased significantly in HS broilers. Moreover, 12α-hydroxylase (CYP8B1) and bile salt export protein (BSEP) were upregulated in the liver, and the expression of fibroblast growth factor 19 (FGF19) decreased in the ileum of HS broilers. There were also significant changes in gut microbial composition, and the enrichment of Peptoniphilus was positively correlated with the increased serum level of TLCA. These results indicate that chronic HS disrupts the homeostasis of BA metabolism in broilers, which is associated with alterations in gut microbiota.

The pathogenesis of gut microbiota in hepatic encephalopathy by the gut-liver-brain axis.

Hepatic encephalopathy (HE) is a neurological disease occurring in patients with hepatic insufficiency and/or portal-systemic blood shunting based on cirrhosis. The pathogenesis is not completely clear till now, but it is believed that hyperammonemia is the core of HE. Hyperammonemia caused by increased sources of ammonia and decreased metabolism further causes mental problems through the gut-liver-brain axis. The vagal pathway also plays a bidirectional role in the axis. Intestinal microorganisms play an important role in the pathogenesis of HE through the gut-liver-brain axis. With the progression of cirrhosis to HE, intestinal microbial composition changes gradually. It shows the decrease of potential beneficial taxa and the overgrowth of potential pathogenic taxa. Changes in gut microbiota may lead to a variety of effects, such as reduced production of short-chain fatty acids (SCFAs), reduced production of bile acids, increased intestinal barrier permeability, and bacterial translocation. The treatment aim of HE is to decrease intestinal ammonia production and intestinal absorption of ammonia. Prebiotics, probiotics, antibiotics, and fecal microbiota transplantation (FMT) can be used to manipulate the gut microbiome to improve hyperammonemia and endotoxemia. Especially the application of FMT, it has become a new treated approach to target microbial composition and function. Therefore, restoring intestinal microbial homeostasis can improve the cognitive impairment of HE, which is a potential treatment method.

Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay.

Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2 ), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.

Soil microbial community composition along chronosequence of the introduction of Phragmites australis at Suncheon Bay

Vegetations of coastal wetlands play a vital role in providing numerous ecological services to the coastal ecosystem and are also key factors affecting the biogeochemical processes in the soil. The acreage of Phragmites australis is expanding and gradually replacing the Suaeda japonica at Suncheon Bay, Republic of Korea. However, the changes in soil microbial community composition caused by Phragmites introduction is poorly characterized. In the present study, soil cores were collected to a depth of 1m (divided into 10 segments of 10 cm) from Suaeda-vegetated, the boundary of Suaeda- and Phragmites-vegetated, Phragmites-vegetated marshes (after 5 and 10 years of the introduction). These samples were analyzed for physico-chemical characteristics, enzyme activities, soil microbial community (phospholipid fatty acids profiling) and abundance of functional genes related to the methane cycle (mcrA, pmoA and dsrA). Results showed that introduction the of Phragmites increased the water content, pH and dissolved organic carbon content in the soil. The contents of total PLFA and microbial group biomarkers of PLFA were observed to be higher in the surface soil and decreased with soil depth. Early introduction of Phragmites (10 yr) sediments had the significantly highest concentrations of total as well as other microbial biomarkers PLFAs compared with other salt marshes. The relative abundance of biomarker PLFAs of Gram-negative bacteria was significantly higher in Phragmites compared to other salt marshes. The abundance of mcrA was significantly highest in Phragmites salt marshes (10 yr) and mixed salt marshes while the abundance of mcrA, pmoA and dsrA were lowest in Suaeda marshes. Our results reflect the chronological effects of the introduction of Phragmites on the physicochemical and microbial community composition which contribute to establishing the relationship between the plant introduction and soil biogeochemical processes in coastal salt marshes.

Effects of different chemical agents on changes in sediment phosphorus composition and the response of sediment microbial community

Controlling the release of sediment phosphorus (P) using chemical agents is a promising method for controlling internal P in eutrophic lakes. However, mineral P formation and changes in the organic P composition after sediment amendment with P-inactivation agents remain poorly understood. Furthermore, little is known about the changes in the sediment microbial community composition after remediation. Here, various ratios of poly aluminum chloride (PAC) and lanthanum-modified bentonite (LMB) were added to nutrient-rich sediments and incubated. Sequential P extraction, solution/solid-state 31P nuclear magnetic resonance (NMR), and microbial analyses were periodically performed on the inactivated sediments. The results indicate that PAC and LMB effectively reduced sediment iron-bound P and organic P, respectively, markedly increasing the content of aluminum- and calcium-bound P in the sediment, respectively. Solid-state 31P NMR results confirmed the formation of rhabdophane (LaPO4. nH2O) in the LMB-amended sediment. Solution 31P NMR results showed that PAC preferentially reduced the organic P fractions of pyrophosphate, whereas LMB efficiently reduced the organic P fractions of orthophosphate, monoesters, and diesters in the sediment. Compared with the control sediment, PAC addition can cause short-term negative effects on sediment microbes at high doses, whereas LMB addition can increase bacterial diversity or richness in the sediment. These results provide a deeper understanding of the differences between PAC and LMB in internal sediment P control.

Biodegradable polymers boost reproduction in the earthworm Eisenia fetida

Microplastic contamination in soil has become a global environmental threat as it adversely affects terrestrial organisms like earthworms as well as soil properties. Especially biodegradable polymers have recently been used as an alternative to conventional polymer types, although their impact remains poorly understood. Thus, we studied the effect of conventional (polystyrene: PS, polyethylene terephthalate: PET, polypropylene: PP) versus aliphatic polyesters classified as biodegradable polymers (poly-(l-lactide): PLLA, polycaprolactone: PCL) on the earthworm Eisenia fetida and soil properties (pH and cation exchange capacity). We addressed direct effects on the weight gain and reproductive success of E. fetida, and indirect effects, like changes in the gut microbial composition as well as the production of short-chain fatty acids by the gut microbiota. Earthworms were exposed for eight weeks in an artificial soil amended with two environmentally relevant concentrations (1 % and 2.5 % (w/w)) of the different microplastic types. PLLA and PCL boosted the number of cocoons produced by 135 % and 54 %, respectively. Additionally, exposure to these two polymers increased number of hatched juveniles, changed gut microbial beta-diversity, and increased the production of the short chain fatty acid lactate compared to the control treatments. Interestingly, we also found a positive effect of PP on the earthworm's bodyweight and reproductive success. The interaction of microplastic and earthworms decreased soil pH by about 1.5 units in the presence of PLLA and PCL. No polymer effect on the cation exchange capacity of soil was found. In general, neither the presence of conventional nor biodegradable polymers had any adverse effects on any of the studied endpoints. Our results suggest that the effects of microplastic highly depend on the polymer type, and that the degradation of biodegradable polymers might be enhanced in the gut of earthworms, which implies that they may use biodegradable polymers as a potential carbon source.

Maternal diet and gut microbiome composition modulate early‐life immune development

In early life, the intestinal mucosa and immune system undergo a critical developmental process to contain the expanding gut microbiome while promoting tolerance toward commensals, yet the influence of maternal diet and microbial composition on offspring immune maturation remains poorly understood. We colonized germ‐free mice with a consortium of 14 strains, fed them a standard fiber‐rich chow or a fiber‐free diet, and then longitudinally assessed offspring development during the weaning period. Unlike pups born to dams fed the fiber‐rich diet, pups of fiber‐deprived dams demonstrated delayed colonization with Akkermansia muciniphila, a mucin‐foraging bacterium that can also use milk oligosaccharides. The pups of fiber‐deprived dams exhibited an enrichment of colonic transcripts corresponding to defense response pathways and a peak in Il22 expression at weaning. Removal of A. muciniphila from the community, but maintenance on the fiber‐rich diet, was associated with reduced proportions of RORγt‐positive innate and adaptive immune cell subsets. Our results highlight the potent influence of maternal dietary fiber intake and discrete changes in microbial composition on the postnatal microbiome assemblage and early immune development.

Fecal metabonomics combined with 16S rDNA sequencing to analyze the changes of gut microbiota in rats fed with different protein source diets.

When blended, animal and plant proteins can complement each other in terms of amino acid composition and release time. In this study, we investigated whether the blended protein diet has a better feeding effect than the single protein diet, and to reveal the differences in growth and intestinal microbiota composition caused by the blended protein diet. Forty Sprague Dawley (SD) rats received diets with different protein sources, including casein (C), whey protein (WP), black soybean protein (BSP), and black soybean-whey blended protein (BS-WP), for eight weeks. To investigate the effects of blended protein supplement on gut microbiota and metabolites, we performed a high throughput 16S rDNA sequencing and fecal metabolomics profiling. In addition, we determined growth and serum biochemical indices, and conducted intestinal morphology analyses. Compared to those in the BSP and WP groups, the daily body weight gain and feed conversion efficiency increased in the BS-WP group. Serum biochemical indices indicated that the protein utilization efficiency of the WP and BS-WP groups was relatively high, and the BS-WP blended protein diet improved the protein adoption rate. The BS-WP blended protein diet also improved intestinal tissue morphology and promoted intestinal villi development compared to the single protein diets. Furthermore, dietary protein altered the composition of gut microbiota, the gut microbial diversity of rats fed with the BS-WP diet was significantly (P < 0.05) higher than that of the other groups. The difference in dietary protein corresponded with an alteration of fecal amino acids and their metabolites, and tryptophan and tyrosine metabolism were the key mechanisms leading to the changes in fecal microbial composition. Dietary protein sources played an important role in the growth and development of rats by influencing intestinal metabolism and microbial composition. The BS-WP blended protein diet was more conducive to nutrient absorption than the single protein diet. Furthermore, blended protein increased the diversity of intestinal microbes and aided the establishment of intestinal barrier function.

High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients

Discerning the effect of pharmacological exposures on intestinal bacterial communities in cancer patients is challenging. Here, we deconvoluted the relationship between drug exposures and changes in microbial composition by developing and applying a new computational method, PARADIGM (parameters associated with dynamics of gut microbiota), to a large set of longitudinal fecal microbiome profiles with detailed medication-administration records from patients undergoing allogeneic hematopoietic cell transplantation. We observed that several non-antibiotic drugs, including laxatives, antiemetics, and opioids, are associated with increased Enterococcus relative abundance and decreased alpha diversity. Shotgun metagenomic sequencing further demonstrated subspecies competition, leading to increased dominant-strain genetic convergence during allo-HCT that is significantly associated with antibiotic exposures. We integrated drug-microbiome associations to predict clinical outcomes in two validation cohorts on the basis of drug exposures alone, suggesting that this approach can generate biologically and clinically relevant insights into how pharmacological exposures can perturb or preserve microbiota composition. The application of a computational method called PARADIGM to a large dataset of cancer patients' longitudinal fecal specimens and detailed daily medication records reveals associations between drug exposures and the intestinal microbiota that recapitulate invitro findings and are also predictive of clinical outcomes.

Denitrification shifted autotroph-heterotroph interactions in Microcystis aggregates

Denitrification is the most important process for nitrogen removal in eutrophic lakes and was mostly investigated in lake sediment. Denitrification could also be mediated by cyanobacterial aggregates, yet how this process impacts nitrogen (N) availability and the associated autotroph-heterotroph relationships within cyanobacterial aggregates has not been investigated. In this study, incubation experiments with nitrate amendment were conducted with Microcystis aggregates (MAs). Measurement of nitrogen contents, 16S rRNA-based microbial community profiling and metatranscriptomic sequencing were used to jointly assess nitrogen turnover dynamics, as well as changes in microbial composition and gene expression. Strong denitrification potential was revealed, and maximal N removal was achieved within two days, after which the communities entered a state of severe N limitation. Changes of active microbial communities were further promoted both with regard to taxonomic composition and transcriptive activities. Expression of transportation-related genes confirmed competition for N sources by Microcystis and phycospheric communities. Strong stress response to reactive oxygen species by Microcystis was revealed. Notably, interspecific relationships among Microcystis and phycospheric communities exhibited a shift toward antagonistic interactions, particularly evidenced by overall increased expression of genes related to cell lysis and utilization of cellular materials. Patterns of fatty acid and starch metabolism also suggested changes in carbon metabolism and cross-feeding patterns within MAs. Taken together, this study demonstrated substantial denitrification potential of MAs, which, importantly, further induced changes in both metabolic activities and autotroph-heterotroph interactions. These findings also highlight the key role of nutrient condition in shaping autotroph-heterotroph relationships.