Abundance Of Archaea Research Articles

Threshold responses of soil gross N transformation rates to aridity gradient.

The responses of soil nitrogen (N) transformations to climate change are crucial for biome productivity prediction under global change. However, little is known about the responses of soil gross N transformation rates to drought gradient. Along an aridity gradient across the 2700 km transect of drylands on the Qinghai-Tibetan Plateau, this study measured three main soil gross N transformation rates in both topsoil (0-10 cm) and subsoil (20-30 cm) using the laboratorial 15 N labelling. The relevant soil abiotic and biotic variables were also determined. The results showed that gross N mineralization and nitrification rates steeply decreased with increasing aridity when aridity was less than 0.5 but just slightly decreased with increasing aridity when aridity was larger than 0.5 at both soil layers. In topsoil, the decreases of the two gross rates were accompanied by the similar decreased patterns of soil total N content and microbial biomass carbon with increasing aridity (p<0.05). In subsoil, although the decreased pattern of soil total N with increasing aridity was still similar to the decreases of the two gross rates (p<0.05), microbial biomass carbon did not change (p>0.05). Instead, bacteria and ammonia oxidizing archaea abundances decreased with increasing aridity when aridity was larger than 0.5 (p<0.05). With an aridity threshold of 0.6, gross N immobilization rate increased with increasing aridity in wetter region (aridity<0.6) accompanied with an increased bacteria/fungi ratio, but decreased with increasing aridity in drier region (aridity>0.6) where mineral N and microbial biomass N also decreased at both soil layers (p<0.05). This study provided new insight to understand the differential responses of soil N transformation to drought gradient. The threshold responses of the gross N transformation rates to aridity gradient should be noted in biogeochemical models to better predict N cycling and manage land in the context of global change.

Genome-centric metagenomic analysis revealed the microbial shifts in response to long-chain fatty acids (LCFA) in anaerobic digestion with hydrochar

Excessive long-chain fatty acids (LCFA) concentration inhibits the normal operation of anaerobic digestion (AD), while the influence of the concentration changes on the microbial communities in the AD has not been explored. In this study, three concentrations (0.25 gCOD/L, 0.5 gCOD/L, 1 gCOD/L) of oleate were investigated in AD to reveal the changes of microbial communities, and hydrochar (HC) was used as an additive to enhance the degradation of oleate in AD. The control groups were unable to maintain stable methanogenesis at all oleate concentrations after the second batch cultivation. However, the addition of HC effectively promoted the methanogenesis under all concentration conditions in the two consecutive batch cultivation. Microbial analysis of AD with HC showed that the relative abundances of Proteobacteria and Firmicutes were increased with increasing oleate concentration and the genus Azospira and genus Methanobacterium were the most abundant bacteria and archaea among the three groups, respectively. Genome-centric metagenomic analysis identified two previously unreported LCFA-degrading bacteria, namely Bin5 Azospira oryzae and Bin82 Pseudomonas balearica. Several microbes were significantly enriched at high oleate concentrations, which might be due to their possession of genes related to DNA repair, maintaining osmotic adjustment, pH homeostasis, and peptidoglycan and liposaccharide biosynthesis.

Enhancement of anaerobic digestion of rice straw by amino acid-derived ionic liquid

This study proposes a novel method to enhance methane production from anaerobic digestion using an amino acid-derived ionic liquid, glycine hydrochloride, ([Gly][Cl]), as an exogenous additive. After 40 days of digestion with 5% [Gly][Cl], the cumulative methane production was 115.56 mL/g VS, which was 73% higher than that of the control group (without additive). Specifically, the peak activities of cellulase, xylanase, and lignin peroxidase were significantly higher than those of the control group. The addition of [Gly][Cl] increased bacterial diversity and reduced archaeal diversity. Synergistota represented by Syner-01, Fibrobacterota represented by BBMC-4, Bacteroides, and unclassified_f__Lachnospiraceae significantly increased in relative abundance. It suggested that [Gly][Cl] stimulated the activities of protein-hydrolyzing and acid-producing bacteria. [Gly][Cl] also increased the abundance of methanogens and archaea, converting more lignocellulose to methane. Methanobacterium, that metabolizes H2 and CO2 to CH4, was more abundant. Therefore, [Gly][Cl] can improve methane yield as an anaerobic digestion additive.

Crop diversification improves the diversity and network structure of the prokaryotic soil microbiome at conventional nitrogen fertilization

BackgroundSustainable agriculture seeks to optimize the application of nitrogen (N) fertilizers to reduce adverse economic and ecological effects. Crop diversification has been proposed to increase the efficiency of N fertilization. An open question is how the soil microbiome responds to these beneficial practices.MethodsIn a field study we investigated the effects of mineral N fertilizer with a 0-control, a conventional amount of 150 kg N ha−1 and an excessive application of 250 kg N ha−1 on the soil microbiome within a diversified cropping system with oil radish and undersown ryegrass over a period of 2.5 years and a non-diversified control, both in rotation of potato, winter rye and maize.ResultsN-fertilizations and crop rotations altered the pH, but differences were less pronounced with the diversified system. Compared to the crop species and season, N fertilization and crop diversification had less influence on the abundance of soil bacteria, archaea and fungi. The crop diversification showed a much stronger effect on archaeal than on bacterial or fungal abundances, while the microbial carbon use efficiency correlated strongly with bacterial abundance. At the end of the growing seasons, crop diversification increased prokaryotic richness and Shannon diversity in response to N addition, with a greater increase in the conventional N. At conventional N supply, prokaryotic co-occurrence networks revealed a much denser and complex structure in the diversified system.ConclusionsThe diversified cropping system under conventional N application rates showed positive effects on the prokaryotic soil microbiome by increasing their richness, Shannon diversity, and promoting a more elaborated network structure.

Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects.

We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.

Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro – Part 2. Dairy goats

Most mitigation strategies to reduce enteric methane (CH4) production in the rumen induce an excess of rumen dihydrogen (H2) that is expelled and consequently not redirected to the synthesis of metabolites that can be utilised by the ruminant. We hypothesised that phenolic compounds can be potential H2 acceptors when added to the diet, as they can be degraded to compounds that may be beneficial for the animal, using part of the H2 available when ruminal methanogenesis is inhibited. We performed four in vitro incubation experiments using rumen inoculum from Murciano-Granadina adult goats: Experiment 1 examined the inhibitory potential of Asparagopsis taxiformis (AT) at different concentrations (0, 1, 2, 3, 4 and 5% of the substrate on a DM basis) in 24 h incubations; Experiment 2 investigated the effect of a wide range of phenolic compounds (phenol, catechol, resorcinol, hydroquinone, pyrogallol, phloroglucinol, gallic acid and formic acid) at different doses (0, 2, 4, and 6 mM) on rumen fermentation for 24 h; Experiment 3 evaluated the combined effect of each phenolic compound at 6 mM with AT at 2% DM in sequential batch cultures for 5 days; and Experiment 4 examined the dose–response effect of phloroglucinol at different concentrations (0, 6, 16, 26 and 36 mM) combined with AT in sequential batch cultures for 5 days. Results from Experiment 1 confirmed that AT at 2% DM substantially inhibited CH4 production while significantly increasing H2 accumulation and decreasing the acetate:propionate ratio. Results from Experiment 2 showed that phenolic compounds did not negatively affect rumen fermentation at any dose. In Experiment 3, each phenolic compound at 6 mM combined with AT at 2% DM inhibited CH4 production. Phloroglucinol numerically decreased H2 accumulation and significantly increased total gas production (TGP), volatile fatty acid (VFA) production and the acetate:propionate ratio. In Experiment 4, phloroglucinol at increasing doses supplemented with AT at 2% DM significantly decreased H2 accumulation and the abundances of archaea, protozoa and fungi abundances, and increased TGP, total VFA production and the acetate:propionate ratio in a dose-dependent way. In conclusion, combined treatment with AT and phloroglucinol was successful to mitigate CH4 production while preventing the accumulation of H2, leading to an increase in acetate and total VFA production and therefore an improvement in rumen fermentation in goats.

Simultaneous addition of CO2-nanobubble water and iron nanoparticles to enhance methane production from anaerobic digestion of corn straw

In this research, CO2-nanobubble water (CO2-NBW) and iron nanoparticles (Fe0NPs) were added simultaneously to exploit individual advantages to enhance the methanogenesis process from both the stability of anaerobic digestion (AD) system and the activity of anaerobic microorganism aspects. Results showed that the AD performance was enhanced by supplementing with CO2-NBW or Fe0NPs individually, and could be further improved by simultaneous addition of the two additives. The maximum methane yield was achieved in the CO2-NBW + Fe0NPs reactor (141.99 mL/g-VSadded), which increased by 26.16% compared to the control group. Similarly, the activities of the electron transfer system (ETS) and enzyme were improved. The results of microbial community structure revealed that the addition of CO2-NBW and Fe0NPs could improve the abundance of dominant bacteria (Anaerolineaceae, Bacteroidales, and Prolixibacteraceae) and archaea (Methanotrichaceae and Methanospirillaceae). Additionally, the functional metabolic prediction heatmap indicated that metabolic functional genes favorable for AD of corn straw were enhanced.

Sweet chestnut forests under black locust invasion threat and different management: An assessment of stand structure and biodiversity

Sweet chestnut forests in Europe are impacted by management abandonment, non-native species invasions and diseases, among other factors. Understanding the effects of these factors is crucial for forecasting future biodiversity changes, as well as proposing appropriate planning and management strategies. We studied sweet chestnut (Castanea sativa Mill.) and black locust (Robinia pseudoacacia L.) dominated forests within three hilly landscapes (Euganean hills, Montello, and Berici hills) of north-eastern Italy. We surveyed 25 paired sweet chestnut and black locust dominated plots of 100 m2 representing coppice or over-aged stands. We collected and analysed data related to vascular plant composition and richness, soil physical features (moisture content, shear strength and penetration resistance), ammonia-oxidising archaea in the soil, and stand structure features. Composition of vascular plants differed significantly between the two forest types, without the influence of management regime. Soil characteristics did not change comparing forest types, management regimes and their interaction, except for soil moisture that was higher in coppice forests. Ammonia-oxidising archaea abundance was lower in sweet chestnut stands. Sweet chestnut and black locust forests have a similar stand structure. The management regime played a role in determining mean diameter, number of stems and deadwood volume. We suggest adopting a heterogeneous array of silviculture practices to achieve the highest variety of forest structures and plant composition in Mediterranean hilly landscapes, coupled with management practices aimed at black locust control.

Archaeal and Extremophilic Bacteria from Different Archaeological Excavation Sites

Beside natural factors, human activities are important for the development of microbiomes. Thus, local soil bacterial communities are affected by recent activities such as agriculture, mining and industry. In addition, ancient human impacts dating back centuries or millennia have changed soils and can emboss the recent bacterial communities up to now, representing a certain long-term "memory of soil". Soil samples from five different archaeological excavation places were investigated for the presence of Archaea with a Next Generation Sequencing (NGS) analysis of the DNA coding for 16S r-RNA sequences. It was found that the abundance of Archaea differs strongly between less than one and more than 40 percent of bacteria. A Principal Component Analysis (PCA) of all samples shows that the archaeological excavation places can be distinguished from each other by the archaeal component of soil bacterial communities, which presents a typical pattern for each place. Most samples are marked by the dominance of Crenarchaeota, which are presented mainly by ammonia-related types. High contents of Nanoarchaeaota have been observed in one ash deposit of a historical saline and all samples of a historical tannery area. These samples are also marked by a significant presence of Dadabacteria. The specific abundancies of special Archaea-among them ammonia-oxidizing and sulphur-related types-are due obviously to former human activities and support the concept of the "ecological memory of soil".

Assessment of the Pinus koraiensis cone essential oil on methane production and microbial abundance using in vitro evaluation system

The objective of this study was to evaluate the potential of Pinus koraiensis cone essential oil (PEO) on in vitro fermentation, methane (CH4) production and microbiota quantification in three different in vitro experiments. First, the main active compounds present in PEO were identified and quantified. Subsequently, the in vitro fermentation characteristics and CH4 production after PEO supplementation (0.20 g/L) at different ratios of forage-to-concentrate (F:C, 100:0, 70:30, 50:50, 30:70, and 0:100; Experiment 1) were evaluated. At a F:C ratios of 50:50, control (CON) and PEO supplementation led to similar total volatile fatty acid concentrations, while CH4 production (13.7%) significantly reduced. Based on this result, we determined that 50:50 F:C ratio can serve as an appropriate diet ratio to evaluate dose-response PEO supplementation. The effects of three levels of PEO supplementation (0.20, 0.50, and 1.0 g/L) on CH4 production, fermentation, and microbiota were then determined in vitro (Experiment 2). Methane production decreased (P < 0.001) with increasing PEO supplementation, with a reduction of up to 65% at 1.0 g/L levels at 24 h of incubation compared with that in the CON. However, PEO supplementation exhibited adverse effects (P < 0.05) on the abundance of most ciliate protozoa, fungi, and fibrolytic bacteria, including Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens. In contrast, the abundance of CH4-producing archaea (total methanogens and Methanobrevibacter sp. AbM4) was greater (P < 0.05) than that in the CON. Furthermore, the effects of PEO supplementation using in vitro continuous culture system for a total of 16 d (including 7 d for adaptation and 9 d for fermentation; Experiment 3) were examined. Methane production was reduced (P < 0.001) (47.1%) upon PEO supplementation compared with that in the CON. Similar to Experiment 2, in vitro fermentation and microbiota were affected (P < 0.05) in response to PEO supplementation. In all three experiments, butyrate was greater (P < 0.001) under PEO supplementation than that in the CON. In addition, butyrate-producing bacteria (Butyrivibrio proteoclasticus) were less sensitive to PEO and contributed to the increased butyrate in the continuous cultures. However, all three in vitro results showed that reduction in CH4 production was accompanied by decreased fermentation parameters. These results suggest that although PEO supplementation can reduce CH4 production, it can alter in vitro fermentation and microbiota, such that the supplementation of a great concentrations of PEO may not be beneficial to ruminants.

Zearalenone and Its Emerging Metabolites Promptly Affect the Rumen Microbiota in Holstein Cows Fed a Forage-Rich Diet.

The study investigated the short-term effects of a single oral bolus of zearalenone (ZEN) on the rumen microbiota and fermentation patterns in four rumen-cannulated Holstein cows fed a forage diet with daily 2 kg/cow concentrate. During the baseline day, cows received uncontaminated concentrate, followed by ZEN-contaminated concentrate on the second day, and again the uncontaminated concentrate on day three. Free rumen liquid (FRL) and particle-associated rumen liquid (PARL) were collected at different hours post-feeding on all days to analyze the prokaryotic community composition, absolute abundances of bacteria, archaea, protozoa, and anaerobic fungi, as well as short-chain fatty acid (SCFA) profiles. The ZEN reduced the microbial diversity in FRL but not in the PARL fraction. The abundance of protozoa was higher after ZEN exposure in PARL, which may be related to their strong biodegradation capacity that, therefore, promoted protozoal growth. In contrast, α-zearalenol might compromise anaerobic fungi as indicated by reduced abundances in FRL and fairly negative correlations in both fractions. Total SCFA significantly increased in both fractions after ZEN exposure, while the SCFA profile only changed marginally. Concluding, a single ZEN challenge caused changes in the rumen ecosystem soon after intake, including ruminal eukaryotes, that should be the subject of future studies.

Bioaugmentation of the green alga to enhance biogas production in an anaerobic hollow-fiber membrane bioreactor

Anaerobic membrane reactors (AnMBRs) offer an alternative wastewater treatment system, presenting both reclamation of value through biogas production, and efficient treatment of recalcitrant contaminants such as antibiotics from wastewater. The effects of bioaugmentation with the green alga Haematococcus pluvialis on anaerobic treatment of pharmaceutical wastewaters, alleviating membrane biofouling, biogas production and impact on the indigenous microbial communities were evaluated using AnMBRs. The outputs of the bioreactor experiments revealed that bioaugmentation strategies with the green alga increased removal of chemical oxygen demand by 12% and delayed membrane fouling by 25% and increased biogas production by 40%. Furthermore, bioaugmentation with the green alga led to a significant change in relative abundance of archaea and the main methanogenesis pathway shifted from Methanothermobacter to Methanosaeta, accompanied by their respective syntrophic bacteria.

P915 Uncovering the role of Archaea in the pathogenesis of Inflammatory bowel disease

Abstract Background Microbial dysbiosis is a major factor that contributes to the course of Inflammatory Bowel Disease (IBD), a complex class of relapsing-remitting chronic inflammatory diseases. The body's overall homeostasis is significantly influenced by the human microbiota, which is a diverse population of bacteria, viruses, fungi, protists, and archaea. Recent research shows that archaea can affect both health and disease, by directly interacting with the host as well as other members of the microbial community. Although the role of bacteria, viruses, and fungi has already been studied, the archaeome remains the under-discovered part of the gut microbiota, especially in the context of IBD. Methods In this study, we profiled the gut archaea using archaeal 16S rRNA gene region in a cohort of pediatric patients with different forms of IBD including Ulcerative colitis (UC), Crohn’s disease (CD), unclassified IBD (IBDU) and healthy controls. We determined the compositional, diversity, and taxonomic alterations of archaea in pediatric patients with IBD and compared to healthy controls. Results Euryarchaeota, and Crenarchaeota, were the major archaeal phyla identified in our samples, other minor phyla identified were Halobacterota and Thermoplasmatota. At the genus level, Methanobrevibacter and Methanosphaera were the most abundant archaea, respectively. Overall, we did not observe any significant difference in the archeal alpha diversity within the various groups. There was however a significant difference between the overall community structure of the archaea between controls and IBD patients (p&amp;lt;0.05). Conclusion A thorough understanding of the role played by the archaea during the pathogenesis of IBD may open the door to the identification of new processes and, ultimately, the development of creative therapeutic targets that can complement the currently used treatments for IBD patients.

Inclusion of Camelina sativa Seeds in Ewes' Diet Modifies Rumen Microbiota.

Supplementing ruminant diets with unconventional feedstuffs (Camelina sativa seeds; CS) rich in bioactive molecules such as polyunsaturated fatty acids, may prove a potential eco-efficient strategy to manipulate rumen microbiome towards efficiency. Forty-eight ewes were divided into four homogenous groups (n = 12) according to their fat-corrected milk yield (6%), body weight, and age, and were fed individually with concentrate, alfalfa hay, and wheat straw. The concentrate of the control group (CON) had no CS inclusion, whereas the treated groups were supplemented with CS at 60 (CS6), 110 (CS11), and 160 (CS16) g·kg-1 of concentrate, respectively. Rumen digesta was collected using an esophageal tube and then liquid and solid particles were separated using cheesecloth layers. An initial bacteriome screening using next-generation sequencing of 16S was followed by specific microbes targeting with a RT-qPCR platform, which unveiled the basic changes of the rumen microbiota under CS supplementation levels. The relative abundances of Archaea and methanogens were significantly reduced in the solid particles of CS11 and CS16. Furthermore, the relative abundance of Protozoa was significantly increased in both rumen fluid and solid particles of the CS6, whereas that of Fungi was significantly reduced in the rumen particle of the CS16. In rumen fluid, the relative abundance of Fibrobacter succinogens and Ruminobacter amylophilus were significantly increased in the CS6 and CS11, respectively. In the solid particles of the CS11, the relative abundance of Ruminococcus flavefaciens was significantly reduced, whereas those of Butyrivibrio proteoclasticus and Ruminobacter amylophilus were significantly increased. Additionally, the relative abundance of Selenomonas ruminantium was significantly increased in both CS11 and CS16. Consequently, the highest CS content in the concentrate reduced the relative abundance of methanogens without inducing radical changes in rumen microorganisms that could impair ruminal fermentation and ewes' performance.

Long-term effects of soluble and insoluble ferric irons on anaerobic oxidation of methane in paddy soil

Iron-dependent anaerobic oxidation of methane (Fe-AOM) is an important process to reduce methane emissions into the atmosphere. It is well known that iron bioavailability largely influences microbial iron reduction, but the long-term effects of different ferric irons on soil Fe-AOM remain unknown. In this work, paddy soil in the ferruginous zone was collected and inoculated with insoluble ferrihydrite and soluble EDTA-Fe(III) for 420 days. Stable isotope experiments, activity inhibition tests, and molecular biological techniques were performed to reveal the activity, microbial community, and possible mechanism of paddy soil Fe-AOM. The results showed that ferrihydrite was a better electron acceptor for long-term Fe-AOM cultivation. Although EDTA-Fe(III) is highly bioavailable and could stimulate Fe-AOM activity for a short time, it restricted the activity increase in the long term. The abundances of archaea, iron-reducing bacteria (IRB), and gene mcrA largely increased after cultivation, indicating the important roles of mcrA-carrying archaea and IRB. Remarkably, archaeal communities were similar, but bacteria were totally different with different ferric irons. The results of the microbial community and activity inhibition suggested that Fe-AOM was performed likely by the cooperation between archaea (Methanomassiliicoccaceae or pGrfC26) and IRB in the cultures.

Microbiome and virome on indoor surfaces of an Antarctic research ship.

Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods. We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity. Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae. This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.

Effect of PVC microplastics on soil microbial community and nitrogen availability under laboratory-controlled and field-relevant temperatures

Microplastics have been reported to affect soil microbiota and nitrogen cycling under controlled temperature conditions, but their impact under field temperature regimes remains unclear. In this study, we compared the impacts of plasticized polyvinyl chloride (PVC) microplastics in an acidic agricultural soil at laboratory-controlled (25 °C) and field-relevant (outdoor ambient, 2–26 °C) temperature conditions. The results showed that changes in soil indicators were roughly the same under the two temperature conditions after 30 d, with increased NH4+-N content and urease activity, decreased NO3−-N content, potential nitrification rate and ammonia-oxidizing archaea abundance, unaltered bacterial abundance, and significant shifts in bacterial community composition. Probably because microbial activity differed at different temperatures, clear discrepancies were also observed: 1) the lowest observed effect concentration was 0.1 % w/w at 25 °C while it was 0.05 % w/w at ambient temperature; 2) a clear dose-effect relationship was observed at 25 °C but not at ambient temperature; and 3) in addition to a range of bacterial taxa that were commonly influenced by microplastics (e.g., Bradyrhizobium, Burkholderia-Caballeronia-Paraburkholderia, Sinomonas, and Sphingomonas), Amycolatopsis, Nocardia and unclassified Saccharimonadales were more responsive at 25 °C while Bacillus and Mycobacterium for ambient temperature. The findings provide insights into the interaction of microplastics with soil microbes under different temperatures and help to understand the threshold values of plasticized PVC microplastics in soil ecosystems.

Optimized Electrical Stimulation Period Facilitated Microbial Electromethane Generation with CO2 Conversion

In order to improve microbial electromethane generation (mEMG) with CO2 conversion using excess renewable power, an electrical stimulation period was optimized to enrich active microorganisms on a biocathode and directionally strengthened electron transfer with a start-up mode of stepwise-promoted intermittent voltage. A highly adaptive microbial community was enriched on the biocathode for an electrical stimulation period of 1 h with the highest population abundance and diversity of archaea and bacteria. The living cell density and average coverage area ratio on the biocathode were 81.37 and 22.07%, respectively. The tryptophan, fulvic acid, and humic acid substances with peak fluorescence intensities in extracelluar polymers effectively improved electron transport in the mEMG system. The highest area capacitance of the biocathode was 13.96 mF/cm2. The biofilm and solution resistances first decreased to valleys (102.3 and 1.541 Ω) and then increased. The highest faradaic efficiency (95.37%) of CH4 was obtained with 2.35 μmol/L coenzyme F420, leading to an increased CH4 production rate by 39.68%.

Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils.

Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.

Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis.

The occurrence and development of colorectal cancer (CRC) and advanced adenoma (AA) are closely related to the gut microbiome, and AA has a high cancerization progression rate to CRC. Current studies have revealed that bacteriological analysis cannot identify CRC from AA. The objective was to explore microbial targets that could identify CRC and AA from a microecological perspective and to figure out the best way to identify CRC based on fecal microbes. The metagenomic sequencing data were used to describe the gut microbiome profile and analyze the differences between microbial abundance and microbial single nucleotide polymorphism (SNP) characteristics in AA and CRC patients. It was found that there were no significant differences in the diversity between the two groups. The abundance of bacteria (e.g., Firmicutes, Clostridia, and Blautia), fungi (Hypocreales), archaea (Methanosarcina, Methanoculleus, and Methanolacinia), and viruses (Alphacoronavirus, Sinsheimervirus, and Gammaretrovirus) differed between AA and CRC patients. Multiple machine-learning algorithms were used to establish prediction models, aiming to identify CRC and AA. The accuracy of the random forest (RF) model based on the gut microbiome was 86.54%. Nevertheless, the accuracy of SNP was 92.31% in identifying CRC from AA. In conclusion, using microbial SNP was the best method to identify CRC, it was superior to using the gut microbiome, and it could provide new targets for CRC screening. IMPORTANCE There are differences in characteristic microorganisms between AA and CRC. However, current studies have indicated that bacteriological analysis cannot identify CC from AA, and thus, we wondered if there were some other targets that could be used to identify CRC from AA in the gut microbiome. The differences of SNPs in the gut microbiota of intraindividuals were significantly smaller than those of interindividuals. In addition, compared with intestinal microbes, SNP was less affected by time with certain stability. It was discovered that microbial SNP was better than the gut microbiome for identifying CRC from AA. Therefore, screening characteristic microbial SNP could provide a new research direction for identifying CRC from AA.