Soil health, and the closely related terms of soil quality and fertility, is considered as one of the most important characteristics of soil ecosystems. The integrated approach to soil health assumes ...that soil is a living system and soil health results from the interaction between different processes and properties, with a strong effect on the activity of soil microbiota. All soils can be described using physical, chemical, and biological properties, but adaptation to environmental changes, driven by the processes of natural selection, are unique to the latter one. This mini review focuses on fungal biodiversity and its role in the health of managed soils as well as on the current methods used in soil mycobiome identification and utilization next generation sequencing (NGS) approaches. The authors separately focus on agriculture and horticulture as well as grassland and forest ecosystems. Moreover, this mini review describes the effect of land-use on the biodiversity and succession of fungi. In conclusion, the authors recommend a shift from cataloging fungal species in different soil ecosystems toward a more global analysis based on functions and interactions between organisms.
The anaerobic digestion (AD) process has become significant for its capability to convert organic wastewater into biogas, a valuable energy source. Excessive acetic acid accumulation in the anaerobic ...digester can inhibit methanogens, ultimately leading to the deterioration of process performance. Herein, the effect of magnetite particles (MP) as an enhancer on the methanogenic degradation of highly-concentrated acetate (6 g COD/L) was examined through long-term sequential AD batch tests. Bioreactors with (AM) and without (AO) MP were compared. AO experienced inhibition and its methane production rate (qm) converged to 0.45 L CH4/g VSS/d after 10 sequential batches (AO10, the 10th batch in a series of the sequential batch tests conducted using bioreactors without MP addition). In contrast, AM achieved 3–425% higher qm through the sequential batches, indicating that MP could counteract the inhibition caused by the highly-concentrated acetate. MP addition to inhibited bioreactors (AO10) successfully restored them, achieving qm of 1.53 L CH4/g VSS/d, 3.4 times increase from AO10 after 8 days lag time, validating its potential as a recovery strategy for inhibited digesters with acetate accumulation. AM exhibited higher microbial populations (1.8–3.8 times) and intracellular activity (9.3 times) compared to AO. MP enriched Methanosaeta, Peptoclostridium, Paraclostridium, OPB41, and genes related to direct interspecies electron transfer and acetate oxidation, potentially driving the improvement of qm through MP-mediated methanogenesis. These findings demonstrated the potential of MP supplementation as an effective strategy to accelerate acetate-utilizing methanogenesis and restore an inhibited anaerobic digester with high acetate accumulation.
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•Magnetite particles MP accelerated CH4 production from highly concentrated acetate.•MP promoted methanogenic degradation of the concentrated acetate by 3–425% in rate.•Inhibited bioreactor was successfully recovered by MP addition with 8d of lag time.•MP stimulated growth and intracellular activity of methanogenic consortia.•Methanosaeta, Paraclostridium and OPB41 contributed to MP-mediated methanogenesis.
Marine bivalves include economically highly important aquacultured species worldwide (oysters, mussels, clams, scallops). Although one third of production in Europe is represented by mussels (Mytilus ...edulis, M. galloprovincialis) a significant decline has been observed in the last two decades, whose causes are likely to be multifactorial, from the presence of pathogens to climate change, often exacerbated by local conditions, leading to mortality outbreaks.
Knowledge of the composition of the microbial communities, together with their relationship with the host, represents a primary target for understanding bivalve health in different environmental conditions. The microbiome is strongly influenced by both local environmental factors and endogenous factors, such as the host immune status. However, information on the seasonal fluctuations of microbial communities in mussels, together with immune parameters, is still lacking.
In the present work, M. galloprovincialis cultivated in north-western Italy (La Spezia) were sampled from February to November 2020 and hemolymph microbiome was evaluated using 16S rRNA gene, together with a set of immune biomarkers in hemocytes (lysosomal membrane stability-LMS, phagocytic activity, ROS production) and soluble lysozyme activity, and parameters of general health conditions (gametogenesis, survival in air).
The results show that M. galloprovincialis hemolymph microbiota was characterized by the constant presence of 8 bacterial genera (Vibrio, Pseudoalteromonas, Tenacibaculum, Colwellia, Shewanella, Amphritea, and 2 from the Arcobacteracea family, Halarcobacter and Arcobacter-like). Seasonal changes in their relative abundance were observed, showing a distinct pattern in winter (February–November) and summer (July, September). Water temperature contributed to shaping the microbiota composition, in particular with regards to the abundance of Vibrios, Psychrilobacter and Photobacterium, Halarcobacter and Arcobacter-like, that was favored by higher temperatures. Seasonal variations of LMS and phagocytosis were also observed, indicating a reduced immunocompetence in winter, concomitant with general stressful conditions associated with spawning. In contrast, the main fluctuations in extracellular immune defences (ROS and lysozyme) were apparently independent of temperature or gametogenic stage. Overall, the results confirm the robustness of mussel immune system, at the same time underlying the potential susceptibility to disease at certain times of the year to additional stressful conditions (i.e. pathogen challenge, pollutant exposure, or further changes in water chemico-physical parameters). These data provide background information useful for monitoring local mussel farming and predicting potential impacts of changing environmental conditions.
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•Study on Mytilus galloprovincialis from an aquaculture site in northwestern Italy.•First data on seasonal changes in hemolymph microbiota and host immune defences.•Increased Vibrio abundance with water T, lower immune defences in winter.•Background info on mussel health status in face of future environmental changes.
Glycerol dialkyl glycerol tetraethers (GDGTs) are widespread but unique membrane-spanning lipids of many Archaea and some Bacteria. However, their specific biological sources and the associated ...environmental controls on their distribution remain unclear, especially in lacustrine settings, hindering our understanding of these compounds and their application as environmental proxies. Here we investigated the GDGT distributions across a large bottom water dissolved oxygen (DO) gradient (0.10–7.20 mg/L) using surface sediments of Lake Yangzonghai, a warm monomictic lake in southwestern China. We show that the distributions of both branched (br) and isoprenoidal (iso) GDGTs co-vary significantly with bottom water DO concentration. The relative abundances of tetramethylated brGDGTs, 5-methyl penta- and hexamethylated brGDGTs and isoGDGT-0 show a stepwise increase as bottom water DO concentration decreases. On the other hand, the relative abundances of 6-methyl penta- and hexamethylated brGDGTs and crenarchaeol exhibit a stepwise decline with a decrease in bottom water DO concentration. Genetic data indicate these DO-induced changes in GDGT parameters are related to changes in the bacterial and archaeal communities across the oxycline in the lake. For example, the high abundance of isoGDGT-0 in low DO samples coincides with a high abundance of methanogenic archaea and Bathyarchaeota. We propose that brGDGT-producing bacteria might include a diversity of other phyla in addition to the proposed source organism acidobacteria; different groups of anaerobic and aerobic bacteria are likely to contribute to the increased abundance of 5-methyl brGDGTs and 6-methyl brGDGTs in low and high DO zones, respectively. Consequently, the MBT′ and MBT′6ME brGDGT indices display strong correlations with DO concentration. Importantly, the MBT′5ME index is not significantly influenced by changes in DO concentration, suggesting that this index might be more resilient to these impacts and more suitable to reconstruct temperature in lake systems.
•One of the most systematic investigation on DO impact on all the GDGT compounds and the related paleoclimate proxies•A new ternary diagram was used to identity the sources of lacustrine brGDGTs•Anaerobic and aerobic bacteria contribute to the increased abundance of 5-methyl and 6-methyl brGDGTs, respectively•MBT′5ME might be more suitable to reconstruct temperature in lake systems than MBT′ and MBT′6ME
Trapa japonica was observed to have inhibiting effects and could be used as a potential environment-friendly control strategy for cyanobacterial blooms in freshwater. However, the changes and ...effecting mechanisms in eukaryotic and prokaryotic communities by T. japonica are not yet clear. In this study, the effects of T. japonica on microbial communities were assessed in Lake Qionghai and Lake Erhai by 18S rRNA and 16S rRNA amplicon sequencing, respectively. The results showed that T. japonica can improve biodiversity and change the microbial community structures to varying degrees in both lakes. The alpha diversity indexes of microbial communities (e.g., Shannon, Sobs, Ace and Chao 1) were higher in the water inhabited by T. japonica (TJ group) than the water uninhabited by T. japonica (control) (P < 0.05). The PCoA results suggested that the microbial community compositions differed between the two groups (PERMANOVA P = 0.001). In Lake Qionghai, the relative abundances of dominant taxa and nutrients level showed little differences between the two groups. These may result from the homogenous water condition in Lake Qionghai. While the genera Cyanobium_PCC-6307, the majority of Cyanobacteria, decreased significantly in TJ group than control according to 16S rRNA gene sequencing. In Lake Erhai, environmental variables were distinctly affected by T. japonica, which was found to drive Cryptophyceae to become the main taxa through taxonomic analysis of 18S rRNA. Based on 16S rRNA gene sequencing, T. japonica reduced the relative abundance of Cyanobacteria, such as Planktothrix_NIVA-CYA_15 and Cyanobium_PCC-6307, by enriching cyanobactericidal bacteria and growth-inhibiting bacteria (e.g., Limnohabitans and Flavobacterium) and changing environmental parameters. Our results revealed that T. japonica acts in shaping microbial communities in lakes on the community level, shedding new lights on eutrophication mitigation, one of the most serious global ecological problems we are facing.
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•A dominant group-shift was driven by Trapa japonica in Lake Erhai.•Trapa japonica can reduce the abundance of Cyanobacteria.•Trapa japonica shapes microbial community structures and improves alpha diversity.
Black-odorous waters (BOWs) are heavily polluted waters where microbial information remains elusive mechanistically. Based on gene amplicon and metagenomics sequencing, a comprehensive study was ...conducted to investigate the microbial communities in urban and rural BOWs. The results revealed that microbial communities’ assembly in urban and rural BOWs was predominantly governed by stochastic factors at the community level. At the taxonomic level, there were 62 core species (58.48%) in water and 207 core species (44.56%) in sediment across urban and rural areas. Notably, significant differences were observed in the functional genetic composition of BOWs between urban and rural areas. Specifically, rural areas exhibited an enhanced abundance of genes involved in nitrogen fixation, Fe2+ transport, and sulfate reduction. Conversely, urban areas showed higher abundances of some genes associated with carbon fixation, nitrification and denitrification. A sulfur-centered ecological model of microbial communities was constructed by integrating data from the three levels of analysis, and 14 near-complete draft genomes were generated, representing a substantial portion of the microbial community (35.04% in rural BOWs and 29.97% in urban BOWs). This research provides significant insights into the sustainable management and preservation of aquatic ecosystems affected by BOWs.
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●The community assembly was dominated by stochastic factors in BOWs.●62 core species in water and 207 core species in sediment were detected.●Metagenomics was used to establish an ecological model in BOWs.●Sulfur metabolism was the core dynamic driving C, N, P and Fe metabolism.
In context of the use of organic materials as alternatives for mineral fertilizer, it is important to understand how organic amendments influence soil extracellular phosphatase activities which ...accelerate the mineralization of organic phosphorus (P). To address this, the current study investigates the influence of organic amendments on acid (ACP) and alkaline (ALP) phosphatase activities in soils and how organic amendments influence these activities from the perspective of microbially-mediated pathways. Herein, a comprehensive meta-analysis of 599 measurements from 106 published studies around the world was performed as well as a field component sourced from a 30-year-old field experiment on fertilization. Based on meta-analysis, organic amendments increased average extracellular ACP and ALP activities by 22% and 53%, respectively, in comparison to the mineral-only fertilization. Observed increases in activities were consistent with significant increases in soil organic carbon (C), total nitrogen (N) and available P contents, and microbial biomass C and N pools. According to the data from the long-term field experiment, we found phoD-harboring species encoding ALP were more closely correlated with phoC-harboring species encoding ACP in organically amended soils, and more network hubs were also observed by organic amendment. Soil C:P and N:P ratios, and microbial biomass C were the main predictors of the abundance, diversity, and composition of the phoC- and phoD-harboring populations. Further analysis revealed that the soil C:P ratio was identified as the dominant predictor of potential ACP and ALP activities. Our work highlights the importance in understanding how soil C:N:P stoichiometry mediates phosphatase-harboring populations in order to determine the downstream consequences of using organic amendments for increasing phosphatase activities.
•We performed a meta-analysis of 599 measurements from 106 published studies with organic amendment.•Organic amendment increased soil phosphatase activity by 22%–53% than mineral-only fertilization.•Phosphatase-harboring microbial populations were tested using phoD and phoC genes.•Stronger co-occurrence pattern existed in the communities of organically amended soils.•Soil C:P ratio and microbial biomass C were the crucial indicator of phosphatase activity.
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•Pollutants were removed via CWs periodically under day-night alterations.•Day-night alterations shifted the rhizosphere microbial community in CWs.•Keystone bacteria relevant to C, ...N, and P metabolism had higher abundance during the daytime.•Microbial metabolism promoted pollutant removal more at night than during the daytime.•Environmental factors exerted a significant influence in driving rhizosphere microbial processes.
Constructed wetlands (CWs), as nature-based wastewater treatment systems, continuously maintain exchanges of material and energy with the natural environment. However, it is unclear how pollutant removal performance in CWs occurs in response to diurnal variation. Herein, we investigated the effects of day-night alterations on the rhizosphere microbial community in CWs. The results revealed that a dynamic alternate mechanism existed in the inner environment when the CWs were in steady operation, which was validated by rhythmic changes in the core microbial community, microbial metabolism activity, and pollutant removal shown in this study. The results showed that pollutant removal (e.g., total nitrogen) due to microbial processes was 1.31 times higher under daytime conditions than under nighttime conditions. Core microbial taxa of the rhizosphere that evolved with circadian rhythm (e.g., Chloroflexus and Beijerinckia) were mostly associated with carbon, nitrogen, phosphorus, and energy metabolism, with lower average relative abundance identified at night. Although higher activity of microbial metabolism was also observed in the daytime, nighttime conditions demonstrated higher gene levels that were related to carbon and nitrogen metabolic functions. Structural equation model (SEM) analysis further suggested that environmental factors exerted a significant influence in driving microbial processes for pollutant removal and that the microbial community played a greater role in promoting pollutant removal under nighttime conditions than under daytime conditions.
Afforestation results in a wide range of soil resources with carbon (C), nitrogen (N), and phosphorus (P) levels that rarely meet microbial elemental demands. Such stoichiometric imbalances result in ...the limitation of microbial activity by nutrients, and have consequences for microbial C and nutrient use efficiency and ultimately the fate of soil C. However, how microorganisms cope with stoichiometric imbalances following afforestation and how their responses regulate microbial-driven C emissions remain unclear. We compared sites along a 42 year Robinia pseudoacacia afforestation chronosequence on the Loess Plateau of China, to quantify soil microbial nutrient limitation and explore the mechanisms underlying microbe-mediated C dynamics under conditions of stoichiometric imbalance. Soil available nutrients, potential activities of C-, N-, and P-acquiring enzymes, microbial biomass, microbial community composition and diversity, as well as microbial respiration were measured. Results showed that stoichiometric imbalances increased soil enzymatic activities targeting the mobilization of limiting nutrients at different afforestation stages. Specifically, soil microbial communities were limited by C in farmland, co-limited by N and P at the 10-year site, and became more limited by P as stand age increased. Reductions in stoichiometric imbalance along the afforestation chronosequence corresponded to an increased microbial alpha diversity and fungi-to-bacteria ratio. Stoichiometric imbalances were more strongly associated with changes in soil bacterial beta diversity than fungal beta diversity. Bacterial communities transitioned from being oligotrophic (Actinobacteria dominant) to copiotrophic (Proteobacteria dominant) during forest development, and this was significantly related to stoichiometric imbalance. However, no significant correlation was detected between stoichiometric imbalance and the dominant fungal phyla (i.e., Ascomycota, Basidiomycota, and Zygomycota). The synergistic responses of enzymatic stoichiometry and microbial community properties to stoichiometric imbalance following afforestation led to reduced microbial threshold elemental ratios, which elevated microbial C use efficiency and increased biomass turnover time, further suppressing microbial respiration. Such collaborative-adaptations imply that more C will be diverted into microbial biomass rather than losing, thus could be favorable to soil C storage. Collectively, these findings highlight the importance of stoichiometric imbalances in regulating microbial-driven C emissions and contribute to an improved understanding of how substrate quality changes induced by revegetation influences terrestrial C flows in ecologically fragile areas.
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•Afforestation lowered stoichiometric imbalances and increased soil enzyme activity.•Afforesting farmland deregulated microbial C limitation but increased P limitation.•Soil bacteria was more sensitive to the C:N:P stoichiometric imbalances than fungi.•Forestation reduced microbial threshold elemental ratios, raising C use efficiency.•Increased microbial C use efficiency and biomass turnover time reduced respiration.
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