Shifts In Microbial Community Structure Research Articles

Co-substrate promoting the biodegradation of refractory DOM in semi-coking wastewater: DOM evolution and microbial community

Semi-coking wastewater treatment has become a difficult issue because of its complexity, heterogeneity and toxicity. In this study, co-metabolism with ethanol or sodium acetate as co-substrates was applied to improve the biological degradation of refractory dissolved organic matter (DOM) in semi-coking wastewater. Kinetic model simulation results indicated that both co-substrates addition improved COD removal efficiency and biodegradation rate. Excitation-emission matrix (EEM) spectroscopy and size exclusion chromatography with organic carbon detector (SEC-OCD) analysis were applied to evaluate the DOM biodegradation in terms of fluorescence and molecular weight (MW). Although co-substrates resulted in a comparable enhanced removal efficiency of protein-like and humic-like fluorophores, there are distinct differences in their specific protein-like fluorescent peaks (Peak C1&C2). Ethanol addition was more conducive to the removal of humic substance with apparent molecular weight (AMW) ranging from 1.1 kDa to 20 kDa. Acetate addition resulted in higher removal of building blocks of humic substances (BB, AMW 0.45–1.1 kDa) and proteinaceous biopolymers (BP, AMW >20 kDa). Co-metabolism triggered the shift of microbial community structure and metabolic functions. Using co-occurrence network analysis, nine keystone genera were identified, which maintained the functional stability of bacterial community responding to organic toxicants stress. LefSe analysis elucidated that the potential major genera involved in refractory organics biodegradation with acetate addition were Stenotrophomonas (40.3%) and Pseudomonas (21.2%), while Pseudoxanthomonas (10.4%) with ethanol addition. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis showed that benzoate, styrene, xylene and naphthalene degradation pathway were enhanced by acetate addition as compared to ethanol.

Elucidation of microbial interactions, dynamics, and keystone microbes in high pressure anaerobic digestion

High-pressure anaerobic digestion (HPAD) is a promising technology for producing biogas enriched with high methane content in a single-step process. To enhance HPAD performance, a comprehensive understanding of microbial community dynamics and their interactions is essential. For this, mesophilic batch high-pressurized anaerobic reactors were operated under 3 bars (H3) and 6 bars (H6). The experimental results showed that the effect of high-pressure (up to 6 bar) on acidification was negligible while methanogenesis was significantly delayed. Microbial analysis showed the predominance of Defluviitoga affiliated with the phylum Thermotogae and the reduction of Thiopseudomonas under high-pressure conditions. In addition, the microbial cluster pattern in H3 and H6 was significantly different compared to the CR, indicating a clear shift in microbial community structure. Moreover, Methanobacterium, Methanomicrobiaceae, Alkaliphilus, and Petrimonas were strongly correlated in network analysis, and they could be identified as keystone microbes in the HPAD reactor.

Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate.

Pit latrines are used by billions of people globally, often in developing countries where they provide a low-tech and low-cost sanitation method. However, health and social problems can arise from a lack of emptying or maintenance of these facilities. A better understanding of the biological and environmental parameters within pit latrines could inform attempts to enhance material decomposition rates, and therefore slow fill-up rate. In this study, we have performed a spatial analysis of 35 Tanzanian pit latrines to identify bacteria and environmental factors that are associated with faster or slower pit latrine fill-up rates. Using ordination of microbial community data, we observed a linear gradient in terms of beta diversity with increasing pit latrine sample depth, corresponding to a shift in microbial community structure from gut-associated families in the top layer to environmental- and wastewater-associated taxa at greater depths. We also investigated the bacteria and environmental parameters associated with fill-up rates, and identified pH, volatile solids, and volatile fatty acids as features strongly positively correlated with pit latrine fill-up rates, whereas phosphate was strongly negatively correlated with fill-up rate. A number of pit latrine microbiota taxa were also correlated with fill-up rates. Using a multivariate regression, we identified the Lactobacillaceae and Incertae_Sedis_XIII taxa as particularly strongly positively and negatively correlated with fill-up rate, respectively. This study therefore increases knowledge of the microbiota within pit latrines, and identifies potentially important bacteria and environmental variables associated with fill-up rates. These new insights may be useful for future studies investigating the decomposition process within pit latrines.

Shift in Microbial Community Structure with Temperature in Deulajhari Hot Spring Cluster, Odisha, India

Hot springs are the reservoirs of novel hyperthermophilic and often mesophilic bacteria that provide information about the prevailing community structure. Here we analyzed the metagenome profile based 16S rRNA amplicon sequencing of the three different springs from Deulajhari hot spring cluster, S1, S2 and S3, having a range of temperature (43°C to 65°C), pH (7.14 – 8.10) and variation in N, P, K, TOC, Salinity, COD and TDS. These thermal spring clusters are covered with the dense vegetation of Pandanus and continuously enriched by plant leaf debris, thus resulting in a high amount of total organic carbon (TOC). The number of phyla varied among the springs: 20 in S1 (43°C), 18 in S2 (55°C) and 24 in S3 (65°C) from the 16S rRNA data. Out of the reported phyla in each spring, the most abundant were Chloroflexi, Proteobacteria, Chlorobi and Acidobacteria, which correlated with the temperature gradient. Various metabolic pathways such as ABC transporters, Two-component system, Purine metabolism were most abundantly present in the S2 sample compared to the other two. The CCA analysis revealed the correlation between physiochemical parameters and their functional annotation. The present study establishes the relation between the physiological parameters and the structural distribution of microbiota along the temperature gradient.

Microbial succession during the degradation of bioplastic in coastal marine sediment favors sulfate reducing microorganisms

Marine environments are sinks for many contaminants, including petroleum-based plastic waste. Bioplastics, or biodegradable plastics derived from renewable resources, are considered promising alternatives as numerous studies have demonstrated their degradation in marine environments. However, their rates of degradation vary and microbial consortia responsible for its degradation are not well characterized. Previous research by our group has shown that polyhydroxyalkanoate (PHA) stimulates sulfate reducing microorganisms (SRM), enriches sulfate reduction gene pools, and accumulates antibiotic and metal resistance genes. Here, we quantify the degradation rate of PHA pellets in marine sediment and present the long-term temporal changes in PHA-associated SRM communities over 424 days. For comparative purposes, polyethylene terephthalate (PET) and ceramic served as biofilm controls and the free-living microorganisms in the overlying water column served as a non-biofilm control. PHA experienced a 51% mass loss after 424 days and a generalized additive mixed model predicted that 100% mass loss would require 909 days. Throughout the course of the 424-day exposure, PHA was colonized by a distinct microbial community while PET and ceramic were colonized by similarly structured communities. SRM comprised a larger proportion of the overall community (25 – 40%) in PHA-associated biofilms as compared to PET and ceramic controls across all timepoints. Further, the diversity of SRM was greater within PHA biofilms than PET and ceramic biofilms. This study shows that PHA degrades relatively slowly and promotes a long-term shift in microbial community structure toward sulfate reduction, demonstrating the ability of this manufactured polymer to alter its environment via the disruption of biogeochemical cycling, indicating that PHA rises to the level of pollutant in benthic marine systems.

A reappraisal of microbiome dysbiosis during experimental periodontitis.

Periodontitis is a chronic inflammatory disease associated with the presence of dysbiotic microbial communities. Several studies interrogating periodontitis pathogenesis have utilized the murine ligature-induced periodontitis (LIP) model and have further examined the ligature-associated microbiome relying on 16S rRNA-based sequencing techniques. However, it is often very challenging to compare microbial profiles across studies due to important differences in bioinformatic processing and databases used for taxonomic assignment. Thus, our study aim was to reanalyze microbiome sequencing datasets from studies utilizing the LIP model through a standardized bioinformatic analysis pipeline, generating a comprehensive overview of microbial dysbiosis during experimental periodontitis.We conducted a reanalysis of 16S rDNA gene sequencing datasets from nine published studies utilizing the LIP model. Reads were grouped according to the hypervariable region of the 16S rDNA gene amplified (V1-V3 and V4), preprocessed, binned into operational taxonomic units and classified utilizing relevant databases. Alpha- and beta-diversity analyses were conducted, along with relative abundance profiling of microbial communities. Our findings revealed similar microbial richness and diversity across studies and determined shifts in microbial community structure determined by periodontitis induction and study of origin. Clear variations in the relative abundance of bacterial taxa were observed starting on day 5 after ligation and onward, consistent with a distinct microbial composition during health and experimental periodontitis. We also uncovered differentially represented bacterial taxa across studies, dominating periodontal health and LIP-associated communities. Collectively, this reanalysis provides a unified overview of microbial dysbiosis during the LIP model, providing new insights that aim to inform further studies dedicated to unraveling oral host-microbial interactions.

気候変動と新興感染症の境界における水産業と水産養殖の持続可能性について：水産疫学は何を提供できるのか？

The global captured fishery is at an all-time low, however, the rising world population and the increase in demand for seafood have led to the rapid growth of the aquaculture industry, including net-pen based salmon production. The aquaculture and fishing industries are challenged by changing ecosystems due to climate change as well as from an increase in the emergence, severity, and prevalence of infectious diseases in the aquatic ecosystem. The potential consequences of farming fish in the vicinity of native wild sympatric fish species is an ongoing debate and has led to the closure of some farm sites in Canada and can have ramifications for other farming regions and species in the absence of a social license. Climate change and infectious diseases are altering the population dynamics of many commercially and culturally important fisheries such as Atlantic and Pacific salmon, lobsters, etc. Many aquatic food animal diseases are associated with pronounced shifts in microbial community structures or genetic and functional changes in reservoir non-virulent progenitor variants. The long-term goal of my research program is to understand the effects of changing ecosystem, and the interaction of farmed and wild fish, by utilizing big data along with appropriate quantitative and epidemiologic tools, on infectious diseases of aquatic food animal species and ultimately to enhance the aquatic epidemiology research program for sustainable aquaculture and fishery. The short-term goal is to conduct prospective and retrospective on-farm (field) or in-silico studies to elucidate the interactions between host, pathogen(s), and environment to understand the occurrence, transmission, and risk factors associated with emerging or likely to emerging infectious diseases in salmon aquaculture and lobster fishery in Canada. Some of the key questions my current research is trying to answer are: what are the spatio-temporal trends in emergence and reemergence of infectious diseases of aquatic food animals, how abundant are non-virulent strains of infectious agents, and how likely are they to convert to virulent strains and result in clinical outbreaks? To what extent do the environmental and other factors interact with these microbial and genetic shifts and result in clinical disease? Are there factors that can be managed to reduce the impact of such diseases? My research uses molecular epidemiology (including microbiome analyses) to evaluate genetic differences between variants and strains of the infectious agents, and profile differences in microbial communities between healthy and clinical fish, applies epidemiological methods to identify the component causes/risk factors (specific agents, genotypes, variants, and strains) involved in the clinical manifestation of these diseases to help understand the complex causal pathway/s of the disease, investigates the association of environmental (water temperature, salinity, dissolved oxygen, and plankton), host (immune system, stress markers), and management factors with outbreaks of the diseases and employs simulation models to evaluate the effectiveness of different control and mitigation measures on the potential spread of infectious diseases between aquaculture sites. I will discuss and present some of my recent studies using these methods that will highlight the importance of epidemiologic research in addressing infectious disease and productivity issues in farmed and wild salmon, lobster, and shrimp.

Biochar induces mineralization of soil recalcitrant components by activation of biochar responsive bacteria groups

Amendment of soil with biochar induces a shift in microbial community structure and promotes faster mineralization of soil organic carbon (SOC), thus offsetting C sequestration effects. Whether biochar induces losses of labile or persistent SOC pools remains largely unknown, and the responsible decomposers await identification. Towards addressing these ends, a C3 soil was amended with Biochar500 or Biochar600 (pyrolyzed at 500 °C and 600 °C, respectively) produced from a C4-maize feedstock and incubated for 28 days. Combination of stable isotope 13C techniques, high-throughput sequencing and Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) allowed changes in soil chemodiversity and biodiversity, as well as their interactive effects on biochar induced SOC mineralization to be elucidated. Results indicated that: i) biochar addition shifted the bacterial community towards dominance of Gemmatimonadetes, Bacteroidia, Alphaproteobacteria and Gammaproteobacteria classes, and coincidence with recalcitrant C components and neutral pH soil; ii) the persistent DOM components (such as condensed aromatics and tannin) were depleted in biochar amended soils, while labile DOM components (such as unsaturated hydrocarbons, lipids, carbohydrates and proteins/amino sugar) were relatively enriched, and; iii) Biochar600 promoted additional soil derived CO2 carbon loss over 28 days (93 mg C kg−1 soil). Collectively, these results suggested that the majority of soil derived CO2 efflux in biochar amended soils originated from recalcitrant components that were mineralized by the persistent organic matter decomposers. This research highlights the significance of biochar responsive taxa in changes of DOM chemodiversity and potential loss of SOC via mineralization.

PLFA Profiling of Coal Mine Spoil: An Integrated Approach for the Assessment of Ecological Restoration

Coal mine overburden spoil created aftermath of mining activities represents disequilibrated geomorphic system. The pedodiversity including its link with biodiversity and landscape ecology describe the spatial diversity has emerged as functional determinants of ecosystem processes. Being the driving force mediating soil processes, ecosystem restoration through mine spoil genesis is monitored based on the shift in microbial community structure in different age series coal mine spoil. Phospholipid fatty acid analysis is culture-independent approach, which provides a set of molecular markers to determine microbial community composition and discriminate microbial communities of different origin. PLFAs are synthesized during microbial growth, rapidly degraded following cell death and reliably reflect living microbial communities. Relative distribution of 51 PLFAs revealed significant variation in microbial community structure across the sites with Shannon diversity index varies from 1.5265 (OB0) to 2.0139 (OB15) and Pielous evenness index from 0.4110 (OB0) to 0.5260 (OB15). Fungal to bacterial ratio exhibited an increasing trend from OB0 (0.055) to OB15 (0.348) over time, which revealed the sign of mine spoil genesis. The principal component analysis and redundancy analysis discriminate different age series coal mine spoil into independent clusters, which evaluated the broad scale patterns of microbial community structure influencing the pace and progress of mine spoil genesis.

Metabarcoding of organic tea (Camellia sinensis L.) chronosequence plots elucidates soil acidification-induced shifts in microbial community structure and putative function

Tea (Camellia sinensis L.) agroecosystem soil acidification (TASA) is occurring at epidemic rates relative to other crops, however TASA remains poorly defined in its pathogenesis and effects on soil microbiota. The present study examined bulk soil physicochemical and bacterial 16S rDNA sequence data to elucidate TASA-associated changes through 10 tea agroecosystem sites, including an organic-certified tea field chronosequence of 3-year- (Young), 8-year- (Middle), and 13-year-old (Old) plots. Soil pH declined linearly with age through chronosequence plots. Hierarchical clustering based on community β-diversity revealed a tipping point in community composition as soil acidified below pH 4.5, which had occurred between Middle and Old plots. Tipping point-associated changes in predicted community functionality included a precipitous decline in nitrogenase-encoding communities and concurrent proliferations of Al-detoxifiers, anti-oxidative specialists, and pathogen virulence factor-encoding communities. PERMANOVA modeling revealed that Streptomyces was the genus with population abundance corresponding most significantly with whole microbiome composition at both OTU- (r2 = 0.460, p < 0.001) and genus-levels (r2 = 0.512, p < 0.001), despite ranking 74th in total abundance among 186 core genera, providing computationally-modeled evidence of a keystone role of Streptomyces under tea agroecosystem conditions. Correlations of soil pH with Rhizobiales (r = 0.713, p < 0.001), Acidibacter (r = −0.717, p < 0.001), and predicted β-glucosidase-encoding communities (r = −0.622, p < 0.001) across all samples indicated potential utility as community-level TASA biomarkers. Moreover, two phylogenetically diverse OTU co-abundance modules also corresponded (p < 0.01) with soil pH across all samples, suggesting that TASA-induced shifts were interfaced by networks of diverse and interactive taxa, or keystone guilds. Presently, organic management per se was unable to retain soil pH within the optimal range for tea plant cultivation (pH 4.5–5.5), therefore additional considerations not currently encompassed by organic management guidelines, such as lower tea planting density, may be necessary to avoid the detrimental effects of soil acidification described above. Moreover, future studies may seek to further elucidate the keystone functions of Streptomyces spp. under tea agroecosystem conditions.

Shifts of microbial community structure along substrate concentration gradients in immobilized biomass for nitrogen removal

Immobilized biomass technology has been regarded as an effective strategy to enhance simultaneous nitrification and denitrification (SND) in existing aerobic biological wastewater treatment processes. Nevertheless, the mechanisms of SND in an aerobic immobilized biomass need to be proven. In this study, waste sludge from municipal wastewater treatment plants was immobilized by cellulose triacetate as bioplates, and an immobilized bioplate reactor (IBPR) was successfully established for nitrogen removal tests. The SND efficiency of the IBPR was increased 18% under the intermittent aeration (IA) mode compared with that under the continuous aeration (CA) mode. During IA operation, the IBPR achieved 96% COD removal and 76% NH4+-N removal, with 71% SND. The results of microbial community analysis by high-throughput sequencing showed that nitrogen-related functional bacteria were more abundant in the bioplates than in the attached biofilms. The colocalization of nitrifiers and denitrifiers in the bioplates was observed, and the microbial community of nitrogen-related functional bacteria clearly shifted with the substrate concentration gradients.

Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants.

Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.

The impact of different voltage application modes on biodegradation of chloramphenicol and shift of microbial community structure

The impact of different voltage application modes on biodegradation of chloramphenicol and shift of microbial community structure

Salinity affects microbial composition and function in artificially induced biocrusts: Implications for cyanobacterial inoculation in saline soils

Cyanobacterial inoculation is a promising technology that can induce biocrust development, for stabilizing degraded soils in dryland environments. However, it is challenging to grow cyanobacteria in dry, saline soils, which limits the application of this technology. In this study, NaCl was added into field-collected induced biocrusts to investigate how salt affects the biocrust community. This fundamental knowledge improves our assessment of microbial salinity preference and adaptation, and can guide researchers to select the appropriate cyanobacterial inoculants for saline soil restoration. The results showed that the biocrusts induced by inoculating Microcoleus vaginatus and Scytonema javanicum could survive 1.0% salinity, although both salt and drought stresses significantly inhibited microbial biomass and metabolism (P < 0.05), and salinity led to an obvious shift in microbial community structure. Compared to salt stress, drought seems to provide a vital ecological protection for the biocrusts, allowing them to be active only under relative low salinity after hydration. In the induced biocrusts, cyanobacteria were always the dominant organisms (even 18 years since inoculation), whereas under elevated salinity, cyanobacterial communities with lower relative abundance had a higher survival percentage of M. steenstrupii and Phormidium sp. Altogether, our results showed that both prokaryotic and eukaryotic communities have obvious salinity preference in the cyanobacteria-induced biocrusts. These results suggest that cyanobacterial inoculation strategies can be adapted in response to the soil salinity conditions. Furthermore, a combined inoculation of M. steenstrupii and Phormidium sp. appears to be favorable approach that is expected to improve cyanobacterial inoculation technology in saline soils.

Eisenia fetida mediated vermi-transformation of tannery waste sludge into value added eco-friendly product: An insight on microbial diversity, enzyme activation, and metal detoxification

Chromium contamination from tannery waste sludge (TWS) is a significant environmental concern. Vermicomposting is useful for conversion of toxic TWS into sanitized nutrient-enriched product for agricultural application. However, interactions among microbes and heavy metals are yet to be studied in Eisenia fetida incubated TWS-based vermireactors. The prime research hypotheses/objectives were to identify the most favorable feedstock combination for efficient vermiremediation; to generate novel information about the microbe-metal interaction during vermicomposting; and justify the functionality E. fetida by studying the TWS-induced shift in microbial community structure, nutrient dynamics, and metal removal. Earthworm population increased by 2.58–2.67 folds in TWS vermibeds. Water soluble and exchangeable fractions of potentially toxic metals (Cr, Pb, Ni, and Cu) considerably reduced by 48–69%. The alkalinity in TWS-dominated feedstocks [TWS + CD (3:1 and 2:1)] was also significantly neutralized with substantial reduction in organic C and increase in NPK availability. Microbial biomass C and different enzyme activities (fluorescein diacetate hydrolysis, urease, phosphatase, sulphatase, and glucosidase) substantially increased in the TWS-vermibeds. Interestingly, PLFA and species diversity analyses revealed that microbial community structure and fatty acid profiles greatly alter depending on the TWS proportion in the feedstocks and the metal-induced stress on microbial communities was substantially low in TWS + CD (1:1) feedstock. The correlation statistics explained that microbial activity and growth have strongly suppressed heavy metal bioavailability in TWS-vermibeds. Overall, the results indicate that TWS + CD (2:1 and 1:1) mixtures were favorable substrates for Eisenia fetida and microbial proliferation. The study revealed new information on microbial influence on metal remediation during vermicomposting and the results suggests that E. fetida could be utilized as a potential candidate for vermiremediation of toxic TWS.

Soil enzymes in response to climate warming: Mechanisms and feedbacks

Abstract Soil enzymes are central to ecosystem processes because they mediate numerous reactions that are essential in biogeochemical cycles. However, how soil enzyme activities will respond to global warming is uncertain. We reviewed the literature on mechanisms linking temperature effects on soil enzymes and microbial communities, and outlined a conceptual overview on how these changes may influence soil carbon fluxes in terrestrial ecosystems. At the enzyme scale, although temperature can have a positive effect on enzymatic catalytic power in the short term (i.e. via the instantaneous response of activity), this effect can be countered over time by enzyme inactivation and reduced substrate affinity. At the microbial scale, short‐term warming can increase enzymatic catalytic power via accelerated synthesis and microbial turnover, but shifts in microbial community composition and growth efficiency may mediate the effect of warming in the long term. Although increasing enzyme activities may accelerate labile carbon decomposition over months to years, our literature review highlights that this initial stage can be followed by the following phases: (a) a reduction in soil carbon loss, due to changing carbon use efficiency among communities or substrate depletion, which together can decrease microbial biomass and enzyme activity and (b) an acceleration of soil carbon loss, due to shifts in microbial community structure and greater allocation to oxidative enzymes for recalcitrant carbon degradation. Studies that bridge scales in time and space are required to assess whether there will be an attenuation or acceleration of soil carbon loss through changes in enzyme activities in the very long term. We conclude that soil enzymes determine the sensitivity of soil carbon to warming, but that the microbial community and enzymatic traits that mediate this effect change over time. Improving representation of enzymes in soil carbon models requires long‐term studies that characterize the response of wide‐ranging hydrolytic and oxidative enzymatic traits—catalytic power, kinetics, inactivation—and the microbial community responses that govern enzyme synthesis. Read the free Plain Language Summary for this article on the Journal blog.

Mixed Effects of Soil Compaction on the Nitrogen Cycle Under Pea and Wheat.

Soil compaction caused by highly mechanized agriculture can constrain soil microbial diversity and functioning. Physical pressure on the soil decreases macropores and thereby limits oxygen diffusion. The associated shift from aerobic to anaerobic conditions can reduce nitrification and promote denitrification processes, leading to nitrogen (N) losses and N depletion that affect plant productivity. High soil moisture content during trafficking can exacerbate the negative effects of soil compaction. However, the extent to which soil moisture amplifies the effects of compaction on the soil microbiome and its control over N cycling is not well understood. Using a controlled greenhouse experiment with two different crops (pea and wheat), we compared the effects of compaction at three different soil moisture levels on soil physicochemical properties, microbial diversity, and the abundance of specific N species and quantification of associated microbial functional groups in the N cycle. Soil compaction increased bulk density from 15% (light compaction) to 25% (severe compaction). Compaction delayed germination in both crops and reduced yield by up to 60% for pea and 40% for wheat. Compaction further induced crop-specific shifts in microbial community structures. After compaction, the relative abundance of denitrifiers increased along with increased nitrate (NO3–) consumption and elevated nitrous oxide (N2O) concentrations in the soil pores. Conversely, the relative abundance of nitrifiers remained stable under compaction, but potentially decelerated nitrification rates, resulting in ammonium (NH4+) accumulation in the soil. This study showed that soil compaction effects are proportional to the initial soil moisture content, which could serve as a good indicator of compaction severity on agricultural fields. However, the impact of soil compaction on crop performance and on microbial communities and functions associated with the N cycle were not necessarily aligned. These findings demonstrate that not only the soil physical properties but also various biological indicators need to be considered in order to provide more precise recommendations for developing sustainable farming systems.

Hemp biochar impacts on selected biological soil health indicators across different soil types and moisture cycles.

Application of crop residues and biochar have been demonstrated to improve soil biological and chemical properties in agroecosystems. However, the integrated effect of organic amendments and hydrological cycles on soil health indicators are not well understood. In this study, we quantified the impact of hemp residue (HR), hemp biochar (HB), and hardwood biochar (HA) on five hydrolytic enzymes, soil microbial phospholipid (PLFA) community structure, pH, permanganate oxidizable carbon (POXC) soil organic carbon (SOC), and total nitrogen (TN). We compared two soil types, Piedmont and Coastal Plain soils of North Carolina, under (i) a 30-d moisture cycle maintained at 60% water-filled pore space (WFPS) (D-W1), followed by (ii) a 7-day alternate dry-wet cycle for 42 days (D-W2), or (iii) maintained at 60% WFPS for 42 days (D-W3) during an aerobic laboratory incubation. Results showed that HR and HB significantly increased the geometric mean enzyme activity by 1-2-fold in the Piedmont soil under the three moisture cycles and about 1.5-fold under D-W in the Coastal soil. In the presence of HA, the measured soil enzyme activities were significantly lower than control under the moisture cycles in both soil types. The shift in microbial community structure was distinct in the Coastal soil but not in the Piedmont soil. Under D-W2, HR and HB significantly increased POXC (600–700 mg POXC kg-1 soil) in the Coastal soil but not in the Piedmont soil while HA increased nitrate (8 mg kg-1) retention in the Coastal soil. The differences in amendment effect on pH SOC, TN, POXC, and nitrate were less distinct in the fine-textured Piedmont soil than the coarse-textured Coastal soil. Overall, the results indicate that, unlike HA, HR and HB will have beneficial effects on soil health and productivity, therefore potentially improving soil’s resilience to changing climate.

Unraveling Nitrogen, Sulfur, and Carbon Metabolic Pathways and Microbial Community Transcriptional Responses to Substrate Deprivation and Toxicity Stresses in a Bioreactor Mimicking Anoxic Brackish Coastal Sediment Conditions

Microbial communities are key drivers of carbon, sulfur, and nitrogen cycling in coastal ecosystems, where they are subjected to dynamic shifts in substrate availability and exposure to toxic compounds. However, how these shifts affect microbial interactions and function is poorly understood. Unraveling such microbial community responses is key to understand their environmental distribution and resilience under current and future disturbances. Here, we used metagenomics and metatranscriptomics to investigate microbial community structure and transcriptional responses to prolonged ammonium deprivation, and sulfide and nitric oxide toxicity stresses in a controlled bioreactor system mimicking coastal sediment conditions. Ca. Nitrobium versatile, identified in this study as a sulfide-oxidizing denitrifier, became a rare community member upon ammonium removal. The ANaerobic Methanotroph (ANME) Ca. Methanoperedens nitroreducens showed remarkable resilience to both experimental conditions, dominating transcriptional activity of dissimilatory nitrate reduction to ammonium (DNRA). During the ammonium removal experiment, increased DNRA was unable to sustain anaerobic ammonium oxidation (anammox) activity. After ammonium was reintroduced, a novel anaerobic bacterial methanotroph species that we have named Ca. Methylomirabilis tolerans outcompeted Ca. Methylomirabilis lanthanidiphila, while the anammox Ca. Kuenenia stuttgartiensis outcompeted Ca. Scalindua rubra. At the end of the sulfide and nitric oxide experiment, a gammaproteobacterium affiliated to the family Thiohalobacteraceae was enriched and dominated transcriptional activity of sulfide:quinone oxidoreductases. Our results indicate that some community members could be more resilient to the tested experimental conditions than others, and that some community functions such as methane and sulfur oxidation coupled to denitrification can remain stable despite large shifts in microbial community structure. Further studies on complex bioreactor enrichments are required to elucidate coastal ecosystem responses to future disturbances.

Two Metatranscriptomic Profiles through Low-Dissolved-Oxygen Waters (DO, 0 to 33 µM) in the Eastern Tropical North Pacific Ocean.

ABSTRACTWe present 16 seawater metatranscriptomes collected from a marine oxygen-deficient zone (ODZ) in the eastern tropical North Pacific (ETNP). This data set will be useful for identifying shifts in microbial community structure and function through oxic/anoxic transition zones, where overlapping aerobic and anaerobic microbial processes impact marine biogeochemical cycling.