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Anthropogenic nitrogen (N) loading alters soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize 68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N-stimulation of nitrification, but does so via climate-related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N-availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate-related shifts in soil ammonia-oxidizing community maintain the N-stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.

Aim Soil microbes can significantly influence restoration outcomes via interaction with plant community assembly processes, yet knowledge about variation in soil microbial communities – in particular functional variation – during oldfield succession is limited. Methods We divided a well-dated successional chronosequence on the Tibetan Plateau into five stages: stage 1 (continued arable land), stage 2 (arable abandoned for 2 years), stage 3 (arable abandoned for 10 years), stage 4 (arable abandoned for 20 years), and natural grassland. We investigated the changes in taxonomic and functional composition of bacterial and fungal communities in these successional stages. Results The richness of bacterial and fungal communities had a unimodal relationship with successional age, as the both were initially low and decreased again in natural grasslands. These changes were more correlated to soil properties. For both bacterial and fungal communities, taxonomic similarity to natural grasslands increased monotonously with successional age. The functional composition of bacterial communities shifted with successional age towards increased importance of strains involved in the C cycle rather than the N cycle, due to higher plant richness. For fungal communities, saprotrophs showed an increasing trend with successional age although low relative abundance in natural grasslands, which was regulated by belowground biomass. Symbiotrophs did not change during succession, but pathotrophic fungal relative abundance decreased rapidly after agricultural abandonment because of increased plant richness. Conclusions Overall, twenty years of oldfield succession did not appear to restore richness of soil bacterial and fungal communities to the levels of natural grasslands. Community taxonomic and functional composition in successional stages up to 20 y old were also different from natural grasslands. Our results suggest more important role of plant com, Aim: Soil microbes can significantly influence restoration outcomes via interaction with plant community assembly processes, yet knowledge about variation in soil microbial communities – in particular functional variation – during oldfield succession is limited. Methods: We divided a well-dated successional chronosequence on the Tibetan Plateau into five stages: stage 1 (continued arable land), stage 2 (arable abandoned for 2 years), stage 3 (arable abandoned for 10 years), stage 4 (arable abandoned for 20 years), and natural grassland. We investigated the changes in taxonomic and functional composition of bacterial and fungal communities in these successional stages. Results: The richness of bacterial and fungal communities had a unimodal relationship with successional age, as the both were initially low and decreased again in natural grasslands. These changes were more correlated to soil properties. For both bacterial and fungal communities, taxonomic similarity to natural grasslands increased monotonously with successional age. The functional composition of bacterial communities shifted with successional age towards increased importance of strains involved in the C cycle rather than the N cycle, due to higher plant richness. For fungal communities, saprotrophs showed an increasing trend with successional age although low relative abundance in natural grasslands, which was regulated by belowground biomass. Symbiotrophs did not change during succession, but pathotrophic fungal relative abundance decreased rapidly after agricultural abandonment because of increased plant richness. Conclusions: Overall, twenty years of oldfield succession did not appear to restore richness of soil bacterial and fungal communities to the levels of natural grasslands. Community taxonomic and functional composition in successional stages up to 20 y old were also different from natural grasslands. Our results suggest more important role of plant community than microbial community to s

Es gibt ein steigendes Interesse an Bakterien-Pilz-Interaktionen, deren Strukturierung, der Kooperation oder Konkurrenz innerhalb dieser Interaktionen und deren ökologischen Folgen (z. B. über entstehende Naturprodukte). Der Schwerpunkt dieser Arbeit lag auf dem Echten Hausschwamm Serpula lacrymans, da dieser Pilz hochspezialisiert auf Bauholz ist und zu den wirtschaftlich wichtigsten Holzzersetzern in Europa gehört. Das Hauptaugenmerk war darauf gerichtet, mehr über die Zusammensetzung der mit S. lacrymans assoziierten mikrobiellen Gemeinschaften und die physiologischen Fähigkeiten der assoziierten Bakterien zu erfahren und herauszufinden, ob es eine von den Interaktionspartnern spezifisch ausgelöste Reaktion von S. lacrymans gibt. Da die Kapazität von mikrobiellen Gemeinschaften, Holz in Innenräumen zu zersetzen, noch nicht umfassend untersucht wurde und S. lacrymans die einzigartig gut entwickelte Fähigkeit besitzt, sich auf Holz zu etablieren und es aggressiv abzubauen, war ein weiteres Hauptziel dieser Arbeit zu untersuchen, ob und wie Bakterien mit dem Pilz beim Holzabbau zusammenarbeiten. Im Folgenden sind die wichtigsten Ergebnisse dieser Dissertation aufgelistet:  Serpula lacrymans hat viele (prokaryotische) Interaktionspartner, die meisten von ihnen sind Gram- positive Bakterien;  Die Bakterien kommen als unabhängige, über das Gewebe verstreute Zellen vor, die keinen Biofilm bilden und nicht als Endosymbionten in den Hyphen vorkommen;  Die Art des pilzlichen Gewebes (Myzelium, Fruchtkörper, Rhizomorph) und die Herkunft der Probe sind die wichtigsten Faktoren, die mikrobielle Vielfalt beeinflussen;  Bakterien können das Wachstum von S. lacrymans in Co-Kultuivierungs-Experimenten hemmen und umgekehrt; außerdem lösen Bakterien die Pigmentproduktion im Pilz aus;  Serpula lacrymans produziert ähnliche Metabolitenmuster, unabhängig davon, ob er mit Pilzen der Gattung Trichoderma oder mit Bakterien unterschiedlicher Taxa konfrontiert wird;  Serpula lacryman, Bacterial-fungal interactions (BFIs), their structuring, the cooperation or competition within, and ecological consequences of them (e.g. via ensuing natural products) have attracted increased attention in recent years. The focus of this work was on the dry rot fungus Serpula lacrymans, as this fungus is highly specialized on building wood and is one of the economically most important timber degraders in Europe. Main emphasis was to learn more about the composition of the microbial community associated with S. lacrymans, the physiological abilities of the associated Prokaryotes, and to gather information on the reaction of the fungus to its interaction partners. As the wood decay ability of indoor microbial communities has not been extensively studied and S. lacrymans has an unique, well-developed capacity to establish on and aggressively degrade wood, one main objective was to investigate if the fungus cooperates with bacteria during wood degradation. The following main results have been obtained:  Serpula lacrymans has many (prokaryotic) interaction partners, most of them are Gram-positive bacteria;  Bacteria appeared as independent cells scattered across and within fungal tissue but do not grew as biofilm; or as endosymbionts of the hyphae;  The type of the fungal tissue (mycelium, fruiting body, rhizomorph) and the sample origins were the main factors influencing prokaryote diversity;  Bacteria could inhibit the growth of S. lacrymans in co-culture experiments, and vice versa. In addition, bacteria triggered pigment production in the fungus;  Serpula lacrymans produced similar metabolite patterns irrespective of a confrontation with fungi of the genus Trichoderma or bacteria from distinct taxa;  Serpula lacrymans hence reacted with a rather general, unspecialized chemical response to biotic stressors, whereby it likely produced acids and/or sugars, alcohols, phenols, or steroids;  Trichoderma spp. and bacteria triggered the biosynthesis of S. lacrymans pi, Abweichender Titel laut Übersetzung der Verfasserin/des Verfassers, Dissertation Universität Innsbruck 2023

Es gibt ein steigendes Interesse an Bakterien-Pilz-Interaktionen, deren Strukturierung, der Kooperation oder Konkurrenz innerhalb dieser Interaktionen und deren ökologischen Folgen (z. B. über entstehende Naturprodukte). Der Schwerpunkt dieser Arbeit lag auf dem Echten Hausschwamm Serpula lacrymans, da dieser Pilz hochspezialisiert auf Bauholz ist und zu den wirtschaftlich wichtigsten Holzzersetzern in Europa gehört. Das Hauptaugenmerk war darauf gerichtet, mehr über die Zusammensetzung der mit S. lacrymans assoziierten mikrobiellen Gemeinschaften und die physiologischen Fähigkeiten der assoziierten Bakterien zu erfahren und herauszufinden, ob es eine von den Interaktionspartnern spezifisch ausgelöste Reaktion von S. lacrymans gibt. Da die Kapazität von mikrobiellen Gemeinschaften, Holz in Innenräumen zu zersetzen, noch nicht umfassend untersucht wurde und S. lacrymans die einzigartig gut entwickelte Fähigkeit besitzt, sich auf Holz zu etablieren und es aggressiv abzubauen, war ein weiteres Hauptziel dieser Arbeit zu untersuchen, ob und wie Bakterien mit dem Pilz beim Holzabbau zusammenarbeiten. Im Folgenden sind die wichtigsten Ergebnisse dieser Dissertation aufgelistet:  Serpula lacrymans hat viele (prokaryotische) Interaktionspartner, die meisten von ihnen sind Gram- positive Bakterien;  Die Bakterien kommen als unabhängige, über das Gewebe verstreute Zellen vor, die keinen Biofilm bilden und nicht als Endosymbionten in den Hyphen vorkommen;  Die Art des pilzlichen Gewebes (Myzelium, Fruchtkörper, Rhizomorph) und die Herkunft der Probe sind die wichtigsten Faktoren, die mikrobielle Vielfalt beeinflussen;  Bakterien können das Wachstum von S. lacrymans in Co-Kultuivierungs-Experimenten hemmen und umgekehrt; außerdem lösen Bakterien die Pigmentproduktion im Pilz aus;  Serpula lacrymans produziert ähnliche Metabolitenmuster, unabhängig davon, ob er mit Pilzen der Gattung Trichoderma oder mit Bakterien unterschiedlicher Taxa konfrontiert wird;  Serpula lacryman, Bacterial-fungal interactions (BFIs), their structuring, the cooperation or competition within, and ecological consequences of them (e.g. via ensuing natural products) have attracted increased attention in recent years. The focus of this work was on the dry rot fungus Serpula lacrymans, as this fungus is highly specialized on building wood and is one of the economically most important timber degraders in Europe. Main emphasis was to learn more about the composition of the microbial community associated with S. lacrymans, the physiological abilities of the associated Prokaryotes, and to gather information on the reaction of the fungus to its interaction partners. As the wood decay ability of indoor microbial communities has not been extensively studied and S. lacrymans has an unique, well-developed capacity to establish on and aggressively degrade wood, one main objective was to investigate if the fungus cooperates with bacteria during wood degradation. The following main results have been obtained:  Serpula lacrymans has many (prokaryotic) interaction partners, most of them are Gram-positive bacteria;  Bacteria appeared as independent cells scattered across and within fungal tissue but do not grew as biofilm; or as endosymbionts of the hyphae;  The type of the fungal tissue (mycelium, fruiting body, rhizomorph) and the sample origins were the main factors influencing prokaryote diversity;  Bacteria could inhibit the growth of S. lacrymans in co-culture experiments, and vice versa. In addition, bacteria triggered pigment production in the fungus;  Serpula lacrymans produced similar metabolite patterns irrespective of a confrontation with fungi of the genus Trichoderma or bacteria from distinct taxa;  Serpula lacrymans hence reacted with a rather general, unspecialized chemical response to biotic stressors, whereby it likely produced acids and/or sugars, alcohols, phenols, or steroids;  Trichoderma spp. and bacteria triggered the biosynthesis of S. lacrymans pi, Julia Embacher, Kumulative Dissertation aus sechs Artikeln, Dissertation Universität Innsbruck 2023

This study was conducted to investigate the capability of the microbial community characteristics and soil variables to promote carbon and nitrogen cycles in maize fields under straw mulch. We covered the surface soil of the maize field with different amounts of wheat straw (0 kg/ha, 2,250 kg/ha, and 4,500 kg/ha) and used 16S rRNA and ITS sequencing, Biology ECO-plate, traditional enzymology, TOC analyzer, and HPLC to measure bacterial and fungal community composition and functions, characteristics of microbial carbon source metabolism, carbon and nitrogen fraction, enzyme activity, and organic acid content in the maize rhizosphere and non-rhizosphere. The results indicated that short-term straw mulch insignificantly affected the alpha diversity of bacterial and fungal communities whereas significantly influenced their beta diversity. The results of functional prediction revealed that straw mulch considerably boosted the relative abundances of bacteria belonging to chemoheterotrophy, aerobic chemoheterotrophy, ureolysis, and nitrogen fixation and inhibited fermentation and nitrate reduction in maize rhizosphere soil. These processes primarily drove the C and N cycles in soil. Straw mulch also improved fungal saprotrophs by raising the proportion of Chaetomiaceae and Chaetosphaeriaceae. The Biology ECO-plate results illustrated that straw mulch weakened the metabolism capacity of microbial labile carbon resources. As a result, the labile C and N fractions were raised under straw mulch. Our results also showed that straw mulch primarily regulated the microbial community structure in rhizosphere soil by significantly decreasing Firmicutes and Ascomycota relative abundance while increasing Basidiomycota. The fungal community structure is more than bacterial for affecting soil microbial biomass carbon, readily oxidizable organic carbon, dissolved organic carbon, available nitrogen, ammonium, and nitrate directly and indirectly through malic acid content and cellulase, pr

To study the effects on coal structure and microbial community diversity during CO2 storage in deep unminable water-bearing coal seams, the lignite in the mining area of Inner Mongolia was selected as the research object. The simulation experiments of supercritical-CO2 (ScCO2)-H2O-microbial-coal interaction under different pressure conditions performed by using an autoclave. Then the solid–liquid phases before and after the reaction were analysed by XPS, low-temperature liquid nitrogen adsorption, 16S rRNA and other testing methods. The results showed that CO2 injection caused the pH and OD600 values in the system to decrease, and the pH and OD600 values in the system decreased more obviously with the increase of ScCO2 pressure. Compared with raw coal, the relative content of carbon elements on the surface of the coal after the reaction increased, and the organic carbon (CC/CH) relative content decreased slightly. In contract, the specific surface area, total pore volume, and the pore size of micropores of coal increased, but the average pore size of the mesopores and macropores decreased. At the same time, with the ScCO2 injection under different pressure conditions, some bacterial cells in the system ruptured and inactivated, resulting in the decrease their relative abundance. In contract, some genera, such as Paraclostridium and Methanoculleus, may have the adaptability to the extreme environment and gradually evolve into the dominant genus. In conclusion, the results provide a theoretical basis for studying the changes of ScCO2 on coal structure and microbial community structure during CO2 storage in deep unminable water-bearing coal seams.

Long-term stability of the aerobic granular sludge system is essentially based on the microbial community structure of the biomass. In this study, the physicochemical and microbial characteristics of sludge and wastewater treatment performance were investigated regarding formation, maturation, and long-term maintenance of granules in two parallel sequencing batch reactors (SBR), R1 and R2, under identical conditions. The aim was to explore the linkage between microbial community structure of the aerobic granules, their long-term stability, as well as the reproducibility of granulation and long-term stability. The two reactors were operated with a COD concentration of 400 mg/L and a chemical oxygen demand to nitrogen (COD/N) ratio of 4:1 under anoxic–oxic conditions. It was found that although SVI30, sludge size, and distributions in R1 and R2 were different, aerobic granules were formed, and they maintained long-term stability in both reactors for 320 days, implying that a certain level of randomness of granulation does not affect the long-term stability and performance for COD and N removal. In addition, a significant reduction in the richness and diversity of microbial production was observed after the sludge was converted from inoculum or flocs to granules, but this did not negatively affect the performance of wastewater treatment. Among the predominant microbial species in aerobic granules, Zoogloea was identified as the most important bacteria present during the whole operation with the highest abundance, while Thauera was the important genus in the formation and maturation of the aerobic granules, but it cannot be maintained long-term due to the low food-to-microorganisms ratio (F/M) in the system. In addition, some species from Ohtaekwangia, Chryseobacterium, Taibaiella, and Tahibacter were found to proliferate strongly during long-term maintenance of aerobic granules. They may play an important role in the long-term stability of aerobic granules. These resul, Peer Reviewed

Constructed wetlands (CWs) are a cost-effective technology for wastewater treatment in which plant-microorganism relationships play a key role in transforming pollutants. However, there is little knowledge about the spatial organization of microbial metabolic processes in CWs. Here we show the structuring of microbial transformation of inorganic sulfur compounds (ISCs) in two horizontal subsurface-flow CW models fed with sulfate-rich artificial wastewater. One model was fully planted with Juncus effusus, while the other was planted only in the middle to investigate further the influence of the plant on ISC transformations. Chemical analyses revealed that sulfate reduction and re-oxidation of sulfide/sulfur occurred simultaneously along the flow paths, with net reduction at the beginning of the CWs, where organic carbon from the influent was still present, and predominant re-oxidation in the downstream sections. Porewater ISC concentrations hardly differed between the two CWs. However, analysis of the bacterial communities showed that sulfur cycling in the fully planted CW was much higher. Total bacterial abundances were about 50 times and 3–4 orders of magnitude higher in the rhizoplane than in porewater and on gravel, respectively, as quantified by qPCR determination of the 16S rRNA gene. Sequencing of 16S rRNA gene amplicons revealed that bacterial communities on the roots and in the porewater differed substantially, apparently a consequence of the fluxes of oxygen and exudates from the roots. Furthermore, we observed partitioning of ISC transforming bacteria into different niches of the CWs. The results of the chemical and microbial analyses collectively support that extensive sulfur cycling occurred in the rhizospheres of the CW models. The study is relevant to the treatment of sulfur-containing wastewater and the elucidation of microbial communities involved in biogeochemical activities to improve water quality.

Global warming is most pronounced in the Arctic region. Greenhouse gas (GHG) release from Arctic soils increase due to global warming. By this, the Arctic may change from currently being a carbon sink to a future source. To improve accurate predictions of future GHG release from Arctic soils, it is important to unravel factors controlling both the microbial community structure and activity. Soil microbial activity is important for Arctic greenhouse gas production, but depends on soil conditions such as salinity being increased by calcium (Ca) and decreased by amorphous silica (Si) potentially enhancing water availability. In the Arctic, climate changes may alter salinity by changing Si and Ca concentrations upon permafrost thaw as a result of global warming with Si potentially decreasing and Ca potentially increasing salinity. Here, we show that higher Si concentration increased and higher Ca concentrations decreased the microbial CO2 production for both a salt-poor and a salt-rich soil from Greenland. In the salt-rich soil, Si amendment increased CO2 production and the abundance of gram-negative bacteria. However, the bacterial community became dominated by spore-forming gram-positive Firmicutes and Actinobacteria. The CO2 release from soils was directly affected by the abundance of bacteria and fungi, and their community structure. Our results highlight the importance of the soil Si and Ca concentration on organic carbon turnover by strongly changing microbial abundance and community structure, with consequences for CO2 release in the Arctic. Consequently, Ca and Si and their relation to Arctic soil microbial community structure has to be considered when estimating pan-Arctic carbon budgets.

Pine wilt disease (PWD) is a worldwide forest disease caused by pine wood nematode (PWN). In this article, we investigated the composition, organization, correlation, and function of the endophytic microbial community in Pinus massoniana field with and without PWN. Samples were taken from branches, upper, middle, and lower trunks, as well as soil, from both healthy and infected trees. The results showed that the fungal diversity of healthy pines is around 1.1 times that of infected pines, while the bacterial diversity is about 0.75 times that of infected pines at the OTUs level. An increase of the abundance of pathogenic fungus such as Saitozyma, Graphilbum, Diplodia, Candida, Pseudoxanthomonas, Dyella and Pantoea was witnessed in infected pines according to the result of LEfSe. Furthermore, Ophiostoma and saprophytic fungus such as Entomocorticium, ganoderma, tomentella, entomocorticium were exclusively prominent in infected pines, which were substantially and highly connected with other species (p < 0.05), indicating the trees’ vulnerability and making the wood blue. In healthy pines, the top three functional guilds are parasites, plant pathogens, and saprotrophs. Parasites (36.52%) are primarily found in the branches, plant pathogens (29.12%) are primarily found in the lower trunk, and saprotrophs (67.88%) are primarily found in the upper trunk of disease trees. Pines’ immunity is being eroded due to an increase in the quantity and types of diseases. PICRUSt2 research revealed that NADH or NADPH, as well as carbon-nitrogen bonds, were more abundant in healthy pines, but acid anhydrides and transferring phosphorus-containing groups were more abundant in infected pines. The shift in resin secretion lowers the tree’s potential and encourages pine wilt and mortality. In total, PWN may have disrupted the microbiological ecology and worked with the community to hasten the demise of pines.

Grazing by livestock can affect plant biodiversity and topsoil functions. However, experimental evidence on whether these impacts are limited to the topsoil or penetrate into deep layers (via changes in soil environment and resource locations) of soil is lacking, especially for soil microbial biomass and diversity. Here, we used paired grazed and ungrazed (fenced) plots at 10 locations across the Mongolian Plateau to investigate how long-term (>10 years) livestock grazing affects the biomass, diversity, composition, and function of microbial communities in surface (0–20 cm) and deep soil layers (40–60 cm). Livestock grazing increased bacterial diversity by 5–9% in both soil layers but increased fungal diversity by 10% only in the topsoil. Livestock grazing also strongly altered bacterial and fungal community composition in both soil layers. Livestock grazing decreased soil C mineralization rates by 11–25% in both soil layers, and decreased soil N mineralization rates by 16% and bacterial biomass by 20% only in the topsoil. The grazing-induced increase in microbial diversity in both soil layers was mainly explained by the changes in plant C:N ratio and plant biomass rather than by soil abiotic variables, especially for the deep soil layer. The grazing-induced negative effects on ecosystem functions (soil C and N mineralization) were mainly associated with soil abiotic variables together with plant variables or microbial diversity in the surface soil layer and were mainly associated with plant variables and soil microbial diversity in the deep soil layer. Overall, our regional field experiment provides the first evidence that the strong effects of livestock grazing on soil microbial biomass, diversity, composition, and function can penetrate the deep soil in arid and semi-arid grasslands. This knowledge suggests that models should consider the dynamic interactions between land use and both soil microbial diversity and biomass across soil depths in global drylands.

Long-term stability of the aerobic granular sludge system is essentially based on the microbial community structure of the biomass. In this study, the physicochemical and microbial characteristics of sludge and wastewater treatment performance were investigated regarding formation, maturation, and long-term maintenance of granules in two parallel sequencing batch reactors (SBR), R1 and R2, under identical conditions. The aim was to explore the linkage between microbial community structure of the aerobic granules, their long-term stability, as well as the reproducibility of granulation and long-term stability. The two reactors were operated with a COD concentration of 400 mg/L and a chemical oxygen demand to nitrogen (COD/N) ratio of 4:1 under anoxic–oxic conditions. It was found that although SVI30, sludge size, and distributions in R1 and R2 were different, aerobic granules were formed, and they maintained long-term stability in both reactors for 320 days, implying that a certain level of randomness of granulation does not affect the long-term stability and performance for COD and N removal. In addition, a significant reduction in the richness and diversity of microbial production was observed after the sludge was converted from inoculum or flocs to granules, but this did not negatively affect the performance of wastewater treatment. Among the predominant microbial species in aerobic granules, Zoogloea was identified as the most important bacteria present during the whole operation with the highest abundance, while Thauera was the important genus in the formation and maturation of the aerobic granules, but it cannot be maintained long-term due to the low food-to-microorganisms ratio (F/M) in the system. In addition, some species from Ohtaekwangia, Chryseobacterium, Taibaiella, and Tahibacter were found to proliferate strongly during long-term maintenance of aerobic granules. They may play an important role in the long-term stability of aerobic granules. These resul, Peer Reviewed

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.

Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the sci

Long-term organic farming aims to reduce synthetic fertilizer and pesticide use in order to sustainably produce and improve soil quality. To do this, there is a need for more information about the soil microbial community, which plays a key role in a sustainable agriculture. In this paper, we assessed the long-term effects of two organic and one conventional cropping systems on the soil microbial community structure using high-throughput sequencing analysis, as well as the link between these communities and the changes in the soil properties and crop yield. The results showed that the crop yield was similar among the three cropping systems. The microbial community changed according to cropping system. Organic cultivation with manure compost and compost tea (Org_C) showed a change in the bacterial community associated with an improved soil carbon and nutrient content. A linear discriminant analysis effect size showed different bacteria and fungi as key microorganisms for each of the three different cropping systems, for conventional systems (Conv), different microorganisms such as Nesterenkonia, Galbibacter, Gramella, Limnobacter, Pseudoalteromonas, Pantoe, and Sporobolomyces were associated with pesticides, while for Org_C and organic cultivation with manure (Org_M), other types of microorganisms were associated with organic amendments with different functions, which, in some cases, reduce soil borne pathogens. However, further investigations such as functional approaches or network analyses are need to better understand the mechanisms behind this behavior.

This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Linköping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH4/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19–29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10 000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS., Funding agencies: Svensk Vatten Utveckling; Tekniska Verken i Linkoping AB; Biogas Research Center; Linkoping University; Swedish Energy AgencySwedish Energy Agency [35624-2]

This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Linköping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH4/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19–29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10 000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS., Funding agencies: Svensk Vatten Utveckling; Tekniska Verken i Linkoping AB; Biogas Research Center; Linkoping University; Swedish Energy AgencySwedish Energy Agency [35624-2]

Hydrolysis is considered to be the rate-limiting step in anaerobic digestion of waste activated sludge (WAS). In this study, an innovative 4 stages cascade anaerobic digestion system was researched to (1) comprehensively clarify whether cascading configuration enhances WAS hydrolysis, and to (2) better understand the governing hydrolysis kinetics in this system. The cascade system consisted of three 2.2 L ultra-short solids retention times (SRT) continuous stirred tank reactors (CSTRs) and one 15.4 L CSTR. The cascade system was compared with a reference conventional CSTR digester (22 L) in terms of process performance, hydrolytic enzyme activities and microbial community dynamics under mesophilic conditions (35 °C). The results showed that the cascade system achieved a high and stable total chemical oxygen demand (tCOD) reduction efficiency of 40–42%, even at 12 days total SRT that corresponded to only 1.2 days SRT each in the first three reactors of the cascade. The reference-CSTR converted only 31% tCOD into biogas and suffered process deterioration at the applied low SRTs. Calculated specific hydrolysis rates in the first reactors of the cascade system were significantly higher compared to the reference-CSTR, especially at the lowest applied SRTs. The activities of several hydrolytic enzymes produced in the different stages revealed that protease, cellulase, amino peptidases, and most of the tested glycosyl-hydrolases had significantly higher activities in the first three small digesters of the cascade system, compared to the reference-CSTR. This increase in hydrolytic enzyme production by far exceeded the increase in specific hydrolysis rate, indicating that hydrolysis was limited by solids-surface availability for enzymatic attack. Correspondingly, high relative abundances of hydrolytic-fermentative bacteria and hydrogenotrophic methanogens as well as the presence of syntrophic bacteria were found in the first three digesters of the cascade system. However, Sanitary Engineering, BT/Biocatalysis

This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Linköping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH4/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19–29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10 000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS., Funding agencies: Svensk Vatten Utveckling; Tekniska Verken i Linkoping AB; Biogas Research Center; Linkoping University; Swedish Energy AgencySwedish Energy Agency [35624-2]

Microbes serve as sensitive indicators of ecosystem change due to their vast diversity and tendency to change in abundance in response to environmental conditions. Although we most frequently observe these changes to study the microbial community itself, it is increasingly common to use them to understand the surrounding environment. In this way microbial communities can be thought of as powerful sensors capable of reporting shifts in chemical or physical conditions with high fidelity. In this commentary, I further explore this idea by drawing a comparison to the olfactory system, where populations of sensory neurons respond to the presence of specific odorants. The possible combinations of sensory neurons that can transduce a signal are virtually limitless. Yet, the brain can deconvolute the signal into recognizable and actionable data. The further development of machine learning techniques and its application hold great promise for our ability to interpret microbes to detect environmental change.

Microbes serve as sensitive indicators of ecosystem change due to their vast diversity and tendency to change in abundance in response to environmental conditions. Although we most frequently observe these changes to study the microbial community itself, it is increasingly common to use them to understand the surrounding environment. In this way microbial communities can be thought of as powerful sensors capable of reporting shifts in chemical or physical conditions with high fidelity. In this commentary, I further explore this idea by drawing a comparison to the olfactory system, where populations of sensory neurons respond to the presence of specific odorants. The possible combinations of sensory neurons that can transduce a signal are virtually limitless. Yet, the brain can deconvolute the signal into recognizable and actionable data. The further development of machine learning techniques and its application hold great promise for our ability to interpret microbes to detect environmental change.

type:Article, Natural attenuation of Mn(II) was observed inside the metal refinery wastewater pipeline, accompanying dark brown-colored mineralization (mostly MnIVO2 with some MnIII 2O3 and Fe2O3) on the inner pipe surface. The Mn-deposit hosted the bacterial community comprised of Hyphomicrobium sp. (22.1%), Magnetospirillum sp. (3.2%), Geobacter sp. (0.3%), Bacillus sp. (0.18%), Pseudomonas sp. (0.03%), and non-metal-metabolizing bacteria (74.2%). Culture enrichment of the Mn-deposit led to the isolation of a new heterotrophic Mn(II)-oxidizer Pseudomonas sp. SK3, with its closest relative Ps. resinovorans (with 98.4% 16S rRNA gene sequence identity), which was previously unknown as an Mn(II)-oxidizer. Oxidation of up to 100 mg/L Mn(II) was readily initiated and completed by isolate SK3, even in the presence of high contents of MgSO4 (a typical solute in metal refinery wastewaters). Additional Cu(II) facilitated Mn(II) oxidation by isolate SK3 (implying the involvement of multicopper oxidase enzyme), allowing a 2-fold greater Mn removal rate, compared to the well-studied Mn(II)-oxidizer Ps. putida MnB1. Poorly crystalline biogenic birnessite was formed by isolate SK3 via one-electron transfer oxidation, gradually raising the Mn AOS (average oxidation state) to 3.80 in 72 h. Together with its efficient in vitro Mn(II) oxidation behavior, a high Mn AOS level of 3.75 was observed with the pipeline Mn-deposit sample collected in situ. The overall results, including the microbial community structure analysis of the pipeline sample, suggest that the natural Mn(II) attenuation phenomenon was characterized by robust in situ activity of Mn(II) oxidizers (including strain SK3) for continuous generation of Mn(IV). This likely synergistically facilitated chemical Mn(II)/Mn(IV) synproportionation for effective Mn removal in the complex ecosystem established in this artificial pipeline structure. The potential utility of isolate SK3 is illustrated for further industrial application in metal r

This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Linköping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH4/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19–29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10 000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS., Funding agencies: Svensk Vatten Utveckling; Tekniska Verken i Linkoping AB; Biogas Research Center; Linkoping University; Swedish Energy AgencySwedish Energy Agency [35624-2]

Patterns of trees’ endogenous rhythmic growth (ERG) and paralleled C allocation shiftbetween root and shoot systems have been studied, but there is still a need to understand theirimpact in shaping soil microbiomes. Moreover, the impact of plants on soil microbial communitiescan be modulated or overweighed by time-induced plant and/or seasonal changes. Thus, weintended to analyze the structure of soil microbiomes as response to simultaneous alternated hosttree root and shoot flushes and time-induced changes within one vegetation period at two sites inCentral Germany. In this study, we utilized oak phytometers (Quercus robur L., clone DF159) as hosttrees, and made use of their ERG, whereby consecutive root and shoot flushes make a completegrowth cycle. We studied two complete growth cycles during the same vegetation period,performed a non-destructive soil sampling and applied high-throughput amplicon sequencing ofthe bacterial 16S gene and the fungal ITS2 region. As C allocation shifts between the tree root andshoot, released root exudates and consequently the nutrient availability alternate for soilmicroorganisms. We therefore anticipated different microbial communities in the host tree root zonealong the growth cycles until autumnal leaf senescence. In our results, the bacterial communityexhibited a directional change over time along the vegetation period. In contrast, the fungalcommunity appeared sample specific. Our findings enlarge the current understanding of thetemporal microbial assembly in the host tree root zone.

Although activated sludge (AS) diffusion is promising for odor control, disagreement still exists on its treatment efficiency of varying odorants, and its microbiological mechanisms remain largely unknown. Herein, we investigated the deodorization efficiency, wastewater treatment performance, and microbiological and ecological effects of AS diffusion in two in situ membrane bioreactors (MBRs). AS diffusion removed ≥ 94.7% of H2S and 100% of NH3, while other odorants were released at low concentrations. The odor-diffused system also achieved appreciable wastewater treatment performance (effluent phosphate at 0.13 ± 0.12 mg/L, COD at 12.1 ± 1.8 mg/L, and total nitrogen at 5.9 ± 1.8 mg-N/L), while membrane fouling was mitigated. Notably, influent wastewater substrates and nutrients, other than MBR system settings, significantly affected system performance, main functional taxa and bacterial community dynamics. Ecological null model and network analysis revealed that odor diffusion strengthened the niche-based deterministic processes (i.e., environmental selection) and caused more negative and intense microbial interactions. Organics competition was enhanced, and some hydrolytic bacteria correspondingly became keystone taxa in the odor-diffused system. The findings provide valuable guidance in establishing efficient AS systems for integrated wastewater and odor treatment.

This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Linköping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH4/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19–29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10 000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS., Funding agencies: Svensk Vatten Utveckling; Tekniska Verken i Linkoping AB; Biogas Research Center; Linkoping University; Swedish Energy AgencySwedish Energy Agency [35624-2]

Hydrolysis is considered to be the rate-limiting step in anaerobic digestion of waste activated sludge (WAS). In this study, an innovative 4 stages cascade anaerobic digestion system was researched to (1) comprehensively clarify whether cascading configuration enhances WAS hydrolysis, and to (2) better understand the governing hydrolysis kinetics in this system. The cascade system consisted of three 2.2 L ultra-short solids retention times (SRT) continuous stirred tank reactors (CSTRs) and one 15.4 L CSTR. The cascade system was compared with a reference conventional CSTR digester (22 L) in terms of process performance, hydrolytic enzyme activities and microbial community dynamics under mesophilic conditions (35 °C). The results showed that the cascade system achieved a high and stable total chemical oxygen demand (tCOD) reduction efficiency of 40–42%, even at 12 days total SRT that corresponded to only 1.2 days SRT each in the first three reactors of the cascade. The reference-CSTR converted only 31% tCOD into biogas and suffered process deterioration at the applied low SRTs. Calculated specific hydrolysis rates in the first reactors of the cascade system were significantly higher compared to the reference-CSTR, especially at the lowest applied SRTs. The activities of several hydrolytic enzymes produced in the different stages revealed that protease, cellulase, amino peptidases, and most of the tested glycosyl-hydrolases had significantly higher activities in the first three small digesters of the cascade system, compared to the reference-CSTR. This increase in hydrolytic enzyme production by far exceeded the increase in specific hydrolysis rate, indicating that hydrolysis was limited by solids-surface availability for enzymatic attack. Correspondingly, high relative abundances of hydrolytic-fermentative bacteria and hydrogenotrophic methanogens as well as the presence of syntrophic bacteria were found in the first three digesters of the cascade system. However, Sanitary Engineering, BT/Biocatalysis

This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Linköping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH4/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19–29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10 000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS., Funding agencies: Svensk Vatten Utveckling; Tekniska Verken i Linkoping AB; Biogas Research Center; Linkoping University; Swedish Energy AgencySwedish Energy Agency [35624-2]

Sludge morphology considerably affects the mechanism underlying microbial anaerobic degradation of phenol. Here, we assessed the phenol degradation rate, specific methanogenic activity, electron transport activity, coenzyme F420 concentration, and microbial community structure of five phenol-degrading sludge of varying particle sizes (i.e., < 20, 20–50, 50–100, 100–200, and > 200 μm). The results indicated an increase in phenol degradation rate and microbial community structure that distinctly correlated with an increase in sludge particle size. Although the sludge with the smallest particle size (< 20 μm) showed the lowest phenol degradation rate (9.3 mg COD·gVSS−1 day−1), its methanogenic activity with propionic acid, butyric acid, and H2/CO2 as substrates was the best, and the concentration of coenzyme F420 was the highest. The small particle size sludge did not contain abundant syntrophic bacteria or hydrogenotrophic methanogens, but contained abundant acetoclastic methanogens. Moreover, the floc sizes of the different sludge varied in important phenol-degrading bacteria and archaea, which may dominate the synergistic mechanism. This study provides a new perspective on the role of sludge floc size on the anaerobic digestion of phenol., Accepted author manuscript, Sanitary Engineering

The herbicide metamitron is frequently detected in the environment, and its degradation in soil differs from that in aquatic sediments. In this study, we applied 13C6-metamitron to investigate the differences in microbial activity, metamitron mineralization and metamitron degrading microbial communities between soil and water-sediment systems. Metamitron increased soil respiration, whereas it suppressed respiration in the water-sediment system as compared to controls. Metamitron was mineralized two-fold faster in soil than in the water-sediment. Incorporation of 13C from 13C6-metamitron into Phospholipid fatty acids (PLFAs) was higher in soil than in sediment, suggesting higher activity of metamitron-degrading microorganisms in soil. During the accelerated mineralization of metamitron, biomarkers for Gram-negative, Gram-positive bacteria and actinobacteria dominated within the 13C-PLFAs in soil. Gram-negative bacteria dominated among the metamitron degraders in sediment throughout the incubation period. Actinobacteria, and actinobacteria and fungi were the main consumers of necromass of primary degraders in soil and water-sediment, respectively.This study clearly showed that microbial groups involved in metamitron degradation depend on the system (soil vs. water-sediment) and on time. It also indicated that the turnover of organic chemicals in complex environments is driven by different groups of synthropic degraders (primary degraders and necromass degraders) rather than by a single degrader.

Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository. Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be > 50% complete and nearly half ≥ 90% complete with ≤ 5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth dynamics for microbes involved in different steps of the food chain. The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.

The mixing zone between high temperature hydrothermal fluids and seawater produces redox gradients, promoting the development of unique ecosystems based on chemotrophy. The structure of microbial communities depends on their environment, which can vary according to space and time. Hydrothermal circulation within the oceanic crust determines the chemical composition and flow of fluids, depending on underground events (earthquakes, volcanic episodes....), and impacts the development of microbial communities. This link between hydrothermal vent communities and deep geological events is the focus of the present study, the first of its kind for slow‐spreading ridge. In this study, we present a unique set of multidisciplinary data collected from 2008 to 2011 on the Eiffel Tower hydrothermal site (Lucky Strike vent field, Mid‐Atlantic Ridge). We benefit from continuous geophysical monitoring (temperature, seismicity) of the site, annual sampling of hydrothermal fluids (hot and diffuse) for geochemistry analyses, sampling of hydrothermal chimneys and an in situ microbial colonization experiments over a year for microbial study. The high CO2 content and concentrations of major elements (Cl, Ca, Si) and SO4 in the end‐member fluids collected in 2010, indicate that a magmatic degassing occurred between 2009 and 2010 under the Lucky Strike hydrothermal field. This is supported by the large temperature variations observed in March‐April 2010. These magmatic CO2 inputs seem to have affected microbial communities’ colonizing the high temperature chimney, as well as the basalts in the more diffuse and mixed zone, promoting the development of thermophilic/anaerobic Archaea and Bacteria (Archaeoglobales, Nautiliales, Nitratiruptoraceae).

The mixing zone between high temperature hydrothermal fluids and seawater produces redox gradients, promoting the development of unique ecosystems based on chemotrophy. The structure of microbial communities depends on their environment, which can vary according to space and time. Hydrothermal circulation within the oceanic crust determines the chemical composition and flow of fluids, depending on underground events (earthquakes, volcanic episodes....), and impacts the development of microbial communities. This link between hydrothermal vent communities and deep geological events is the focus of the present study, the first of its kind for slow‐spreading ridge. In this study, we present a unique set of multidisciplinary data collected from 2008 to 2011 on the Eiffel Tower hydrothermal site (Lucky Strike vent field, Mid‐Atlantic Ridge). We benefit from continuous geophysical monitoring (temperature, seismicity) of the site, annual sampling of hydrothermal fluids (hot and diffuse) for geochemistry analyses, sampling of hydrothermal chimneys and an in situ microbial colonization experiments over a year for microbial study. The high CO2 content and concentrations of major elements (Cl, Ca, Si) and SO4 in the end‐member fluids collected in 2010, indicate that a magmatic degassing occurred between 2009 and 2010 under the Lucky Strike hydrothermal field. This is supported by the large temperature variations observed in March‐April 2010. These magmatic CO2 inputs seem to have affected microbial communities’ colonizing the high temperature chimney, as well as the basalts in the more diffuse and mixed zone, promoting the development of thermophilic/anaerobic Archaea and Bacteria (Archaeoglobales, Nautiliales, Nitratiruptoraceae).

Riverbank filtration (RBF) as a barrier of pathogenic microorganisms and organic micropollutants recently has been proven capable of removing sulfonamides. However, the study about the effect of redox conditions on biodegradation of common and persistent sulfonamides in RBF is limited and the response of microbial communities to sulfonamides stress during RBF is unknown. In this study, two column set-ups (with residence time 5 days and 11 days respectively), simulating different redox conditions of riverbank filtration systems, were operated for seven months to investigate 1) the long-term effect of redox conditions on ng∙L−1 level sulfonamides (sulfapyridine, sulfadiazine, sulfamethoxazole, sulfamethazine, sulfaquinoxaline) removal, and 2) the microbial community evolution represented by the phylogenetic and metabolic function shift under non-lethal selective pressures of sulfonamides. The results showed that sulfonamides were more degradable under anoxic conditions than oxic and suboxic conditions. In the sulfonamides stressed community, the phylogenetic diversity increased slightly. Relative abundance of an intrinsic sulfonamides resistant bacteria Bacillus spp. increased, suggesting that sulfonamide resistance developed in specific bacteria under sulfonamides contamination pressure in RBF systems. At the same time, an activated transport function in the stressed microbial community was noticed. The predicted relative abundance of gene folP, which encodes dihydropteroate synthase, also increased significantly, indicating a detoxification mechanism and sulfonamides resistance potential under non-lethal selective pressures of sulfonamides in RBF systems., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., Sanitary Engineering

The mixing zone between high temperature hydrothermal fluids and seawater produces redox gradients, promoting the development of unique ecosystems based on chemotrophy. The structure of microbial communities depends on their environment, which can vary according to space and time. Hydrothermal circulation within the oceanic crust determines the chemical composition and flow of fluids, depending on underground events (earthquakes, volcanic episodes....), and impacts the development of microbial communities. This link between hydrothermal vent communities and deep geological events is the focus of the present study, the first of its kind for slow‐spreading ridge. In this study, we present a unique set of multidisciplinary data collected from 2008 to 2011 on the Eiffel Tower hydrothermal site (Lucky Strike vent field, Mid‐Atlantic Ridge). We benefit from continuous geophysical monitoring (temperature, seismicity) of the site, annual sampling of hydrothermal fluids (hot and diffuse) for geochemistry analyses, sampling of hydrothermal chimneys and an in situ microbial colonization experiments over a year for microbial study. The high CO2 content and concentrations of major elements (Cl, Ca, Si) and SO4 in the end‐member fluids collected in 2010, indicate that a magmatic degassing occurred between 2009 and 2010 under the Lucky Strike hydrothermal field. This is supported by the large temperature variations observed in March‐April 2010. These magmatic CO2 inputs seem to have affected microbial communities’ colonizing the high temperature chimney, as well as the basalts in the more diffuse and mixed zone, promoting the development of thermophilic/anaerobic Archaea and Bacteria (Archaeoglobales, Nautiliales, Nitratiruptoraceae).

The mixing zone between high temperature hydrothermal fluids and seawater produces redox gradients, promoting the development of unique ecosystems based on chemotrophy. The structure of microbial communities depends on their environment, which can vary according to space and time. Hydrothermal circulation within the oceanic crust determines the chemical composition and flow of fluids, depending on underground events (earthquakes, volcanic episodes....), and impacts the development of microbial communities. This link between hydrothermal vent communities and deep geological events is the focus of the present study, the first of its kind for slow‐spreading ridge. In this study, we present a unique set of multidisciplinary data collected from 2008 to 2011 on the Eiffel Tower hydrothermal site (Lucky Strike vent field, Mid‐Atlantic Ridge). We benefit from continuous geophysical monitoring (temperature, seismicity) of the site, annual sampling of hydrothermal fluids (hot and diffuse) for geochemistry analyses, sampling of hydrothermal chimneys and an in situ microbial colonization experiments over a year for microbial study. The high CO2 content and concentrations of major elements (Cl, Ca, Si) and SO4 in the end‐member fluids collected in 2010, indicate that a magmatic degassing occurred between 2009 and 2010 under the Lucky Strike hydrothermal field. This is supported by the large temperature variations observed in March‐April 2010. These magmatic CO2 inputs seem to have affected microbial communities’ colonizing the high temperature chimney, as well as the basalts in the more diffuse and mixed zone, promoting the development of thermophilic/anaerobic Archaea and Bacteria (Archaeoglobales, Nautiliales, Nitratiruptoraceae).

Leaf litter decomposition is a key component of global biogeochemical cycles that influence soil carbon storage, nutrient availability and plant productivity. Ongoing climate change will lead to warmer and drier conditions in many dryland regions, potentially affecting litter decomposition and nutrient dynamics. Climate change effects can be direct and/or indirect, for example, through changes in litter quality, yet their relative importance on litter decomposition remains unclear. We conducted a manipulative study in a semi-arid shrubland to assess the effects of leaf litter quality, forecasted climate change, that is, +2.5°C warming (W), 30% rainfall reduction (RR) as well as their interaction (W + RR) to elucidate their relative effects on litter decomposition. Climatic effects alone reduced decomposition of a homogeneous Control leaf litter collected from Helianthemum squamatum shrubs growing in unmanipulated plots by 23.4%, 18.1% and 29.8% in the W, RR and W + RR treatments respectively. Leaf litter quality was lower in shrubs that had been growing in warmed plots (W and W + RR), as they had lower nutrient concentrations (P, Fe) and higher C:N and C:P ratios than leaf litter produced under ambient (Control) conditions. Lignin concentration was significantly lower in litter from W + RR plots, yet when both climate and litter quality were considered simultaneously, decomposition rates were 32.0%, 26.3% and 39.9% lower in W, RR and W + RR plots compared to Controls. In addition, we found greater microbial N immobilization in leaf litter incubated within warmed (W and W + RR) than within non-warmed plots (Control and RR). Structural equation modelling showed that higher litter moisture and microbial biomass contents stimulated decomposition. Simulated climate change (W, RR and W + RR) reduced decomposition indirectly by negatively affecting litter moisture contents and litter microbial biomass. Microbial nitrogen immobilization was stimulated by the lower quality (

Riverbank filtration (RBF) as a barrier of pathogenic microorganisms and organic micropollutants recently has been proven capable of removing sulfonamides. However, the study about the effect of redox conditions on biodegradation of common and persistent sulfonamides in RBF is limited and the response of microbial communities to sulfonamides stress during RBF is unknown. In this study, two column set-ups (with residence time 5 days and 11 days respectively), simulating different redox conditions of riverbank filtration systems, were operated for seven months to investigate 1) the long-term effect of redox conditions on ng∙L−1 level sulfonamides (sulfapyridine, sulfadiazine, sulfamethoxazole, sulfamethazine, sulfaquinoxaline) removal, and 2) the microbial community evolution represented by the phylogenetic and metabolic function shift under non-lethal selective pressures of sulfonamides. The results showed that sulfonamides were more degradable under anoxic conditions than oxic and suboxic conditions. In the sulfonamides stressed community, the phylogenetic diversity increased slightly. Relative abundance of an intrinsic sulfonamides resistant bacteria Bacillus spp. increased, suggesting that sulfonamide resistance developed in specific bacteria under sulfonamides contamination pressure in RBF systems. At the same time, an activated transport function in the stressed microbial community was noticed. The predicted relative abundance of gene folP, which encodes dihydropteroate synthase, also increased significantly, indicating a detoxification mechanism and sulfonamides resistance potential under non-lethal selective pressures of sulfonamides in RBF systems., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., Sanitary Engineering

The effect of degraded soil conditions on microbial communities associating the rhizosphere and roots of grapevines was investigated within the frame of project CORE Organic Plus ReSolVe. Several relationships based on Dice cluster analyses of DGGE gel profiles suggest that fungal and bacterial communities from degraded and non-degraded areas differ. Results also suggest that composted organic amendments had an effect on community structures. However, the comparison of diversity indexes did not show differences between degraded and non-degraded plots. They suggested rich and even diversity of bacteria and fungi in any of the tested samples. Culture dependent analysis emphasized that a high diversity of Streptomyces spp. associates grapevine roots in degraded and non-degraded areas. Streptomyces species, best known for their potential to produce antibiotics, are increasingly depicted as beneficial plant associated bacteria.

Nutrient loading is a leading cause of global seagrass decline, triggering shifts from seagrass- to macroalgal-dominance. Within seagrass meadows of Xincun Bay (South China Sea), we found that nutrient loading (due to fish farming) increased sediment microbial biomass and extracellular enzyme activity associated with carbon cycling (polyphenol oxidase, invertase and cellulase), with a corresponding decrease in percent sediment organic carbon (SOC), suggesting that nutrients primed microorganism and stimulated SOC remineralization. Surpisingly, however, the relative contribution of seagrass-derived carbon to bacteria (δ(13)Cbacteria) increased with nutrient loading, despite popular theory being that microbes switch to consuming macroalgae which are assumed to provide a more labile carbon source. Organic carbon sources of fungi were unaffected by nutrient loading. Overall, this study suggests that nutrient loading changes the relative contribution of seagrass and algal sources to SOC pools, boosting sediment microbial biomass and extracellular enzyme activity, thereby possibly changing seagrass blue carbon.

Antibiotic resistance genes (ARGs) in urban rivers are a serious public health concern in regions with poorly planned, rapid development. To gain insights into the predominant factors affecting the fate of ARGs in a highly polluted urban river in eastern China, a total of 285 ARGs, microbial communities, and 20 physicochemical parameters were analyzed for 17 sites. A total of 258 unique ARGs were detected using high-throughput qPCR, and the absolute abundance of total ARGs was positively correlated with total organic carbon and total dissolved nitrogen concentrations (P < 0.01). ARG abundance and diversity were greatly altered by microbial community structure. Variation partitioning analysis showed that the combined effects of multiple factors contributed to the profile and dissemination of ARGs, and variation of microbial communities was the major factor affecting the distribution of ARGs. The disparate distribution of some bacteria, including Bacteroides from mammalian gastrointestinal flora, Burkholderia from zoonotic infectious diseases, and Zoogloea from wastewater treatment, indicates that the urban river was strongly influenced by point-source pollution. Results imply that microbial community shifts caused by changes in water quality may lead to the spread of ARGs, and point-source pollution in urban rivers requires greater attention to control the transfer of ARGs between environmental bacteria and pathogens.

The surface waters at the ultramafic ophiolitic outcrop in Chimaera, Turkey, are characterized by high pH values and high metal levels due to the percolation of fluids through areas of active serpentinization. We describe the influence of the liquid chemistry, mineralogy, and H-2 and CH4 levels on the bacterial community structure in a semidry, exposed, ultramafic environment. The bacterial and archaeal community structures were monitored using Illumina sequencing targeting the 16S rRNA gene. At all sampling points, four phyla, Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria, accounted for the majority of taxa. Members of the Chloroflexi phylum dominated low-diversity sites, whereas Proteobacteria dominated high-diversity sites. Methane, nitrogen, iron, and hydrogen oxidizers were detected as well as archaea and metal-resistant bacteria. IMPORTANCE Our study is a comprehensive microbial investigation of the Chimaera ophiolite. DNA has been extracted from 16 sites in the area and has been studied from microbial and geochemical points of view. We describe a microbial community structure that is dependent on terrestrial, serpentinization-driven abiotic H-2, which is poorly studied due to the rarity of these environments on Earth.

Antibiotic resistance genes (ARGs) in urban rivers are a serious public health concern in regions with poorly planned, rapid development. To gain insights into the predominant factors affecting the fate of ARGs in a highly polluted urban river in eastern China, a total of 285 ARGs, microbial communities, and 20 physicochemical parameters were analyzed for 17 sites. A total of 258 unique ARGs were detected using high-throughput qPCR, and the absolute abundance of total ARGs was positively correlated with total organic carbon and total dissolved nitrogen concentrations (P < 0.01). ARG abundance and diversity were greatly altered by microbial community structure. Variation partitioning analysis showed that the combined effects of multiple factors contributed to the profile and dissemination of ARGs, and variation of microbial communities was the major factor affecting the distribution of ARGs. The disparate distribution of some bacteria, including Bacteroides from mammalian gastrointestinal flora, Burkholderia from zoonotic infectious diseases, and Zoogloea from wastewater treatment, indicates that the urban river was strongly influenced by point-source pollution. Results imply that microbial community shifts caused by changes in water quality may lead to the spread of ARGs, and point-source pollution in urban rivers requires greater attention to control the transfer of ARGs between environmental bacteria and pathogens.

Numerous studies have looked at biotic succession at the aboveground level; however, there are no studies describing fungal community change associated with long-term ecosystem development. To understand ecosystem development, the organisms responsible for shaping and driving these systems and their relationships with the vegetation and soil factors, it is critical to provide insight into aboveground and belowground linkages to ultimately include this new information into ecosystem theory. I hypothesized that fungal communities would change with pedogenesis, that these changes would correlate with vegetation community change, and that they should show change of composition and diversity as the seasons change. Chapter 1 discusses the main topics related to this dissertation. Chapter 2 includes a publication draft that describes a study of sand-dune soil samples from northern Michigan that were analyzed to pinpoint the structural change in the fungal community during the development of the ecosystem. The samples were analyzed by pyrosequencing the soil DNA, targeting the internal transcribed spacer region. Chapter 3 contains a coauthored published paper that describes plant invasion of fields in Virginia to determine how they impact soil bacterial and fungal communities. The bacterial and fungal communities that were invaded by 3 different plant species exhibited similar changes, regardless of plant species, suggesting that some functional traits of invasives may have similar impacts on belowground communities. Chapter 4 remarks the conclusions of this research.

With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples of the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.

The degradation characteristics of carbendazim (CBD) and chlortetracycline (CTC) in individual and combined treatments, and dynamics of soil microbial structural and functional diversity as well as their potential relations were studied during three repeated treatments using different concentrations. The results showed that the degradation half-life of CBD at concentrations of 3 mg/kg and 6 mg/kg obviously increased, but that of CTC at levels of 1 mg/kg and 10 mg/kg decreased with increasing treatment frequency. Soil microbial activity and functional diversity displayed the suppression trend in CBD treatment and the suppression-recovery-stimulation trend in CTC and CBD + CTC treatments, which were consistent with the findings of decreased degradation rate of CBD and increased degradation rate of CTC. 16S amplicon sequencing analysis revealed five potentially dominant CTC-resistant microbial genera including Bacillus, Actinobacillus, Pseudomonas, Mycobacterium, and Corynebacterium, which may mainly carry major facilitator superfamily transporter protein, ribosomal protection protein, and other proteins encoded by tetA, tetB, tetC, tetH, tetL, tetM, tetO, tetV, tetW, tetX, tetZ, tet33, and tet39. These five dominant genera may jointly contribute to the elevated bacterial community resistance to CTC. Our findings provided a better understanding of microbial community structure and function changes in repeatedly treated soils with CBD and CTC. © 2016 Elsevier B.V.