Shifts In Microbial Community Structure Research Articles

Shifts in microbial community structure influence the availability of Fe and other micronutrients to lupin (Lupinus albus L.)

Soil microorganisms may play a pivotal role in the uptake of Fe and other micronutrients by plants. However, direct evidence of the effects of changes in microbial community structure on micronutrient availability to plants is scant. In this work, we hypothesized that shifts in microbial community structure and diversity in soil influence Fe availability to lupin plants. To obtain samples from the same soil with different microbial community structure, in October 2009 we sampled the surface horizon (0–0.1 m deep layer) of a calcareous (Chromic Haploxerert) soil under an ongoing long-term (27 yr) tillage experiment in southern Spain involving conventional tillage with soil inversion (CT) and no-till (NT). Samples of CT and NT soil were used to grow white lupin (Lupinus albus L.) under controlled conditions, and the concentration and total contents in micronutrients of plant shoots taken to be indicators of their availability in soil.The total contents in Fe, Cu, Mn and Zn of shoots increased with increasing number of colony forming units (CFU) of oligotrophic bacteria, which explained around 90% of the variability of Fe and Cu in shoots (P < 0.01). Soil under CT had five times greater CFU counts of oligotrophic bacteria (P < 0.001) and showed higher microbial diversity than soil under NT. These results account for the increased concentrations and total contents of Fe, Mn, and Cu in shoots of lupin grown on soil under CT relative to NT (41, 40 and 88% higher, respectively; P < 0.05). The total plant contents of nutrients were related to neither the total number of viable cells nor the biochemical parameters associated to microbial activity, which were greater under NT than under CT. Therefore, the population of oligotrophic bacteria in soil, which was affected by tillage method, has a marked influence on micronutrient availability to plants.

Anaerobic treatment of LCFA-containing synthetic dairy wastewater at 20 °C: Process performance and microbial community dynamics.

Facilitating anaerobic degradation of long-chain fatty acids (LCFA) is key for tapping the high methane production potential of the fats, oil and grease (FOG) content of dairy wastewaters. In this study, the feasibility of using high-rate granular sludge reactors for the treatment of mixed LCFA-containing synthetic dairy wastewater (SDW) was assessed at 20 °C. The effects of the LCFA concentration (33-45% of COD) and organic loading rates (2-3 gCOD/L·d) were determined using three parallel expanded granular sludge bed reactors. For the first time, long term anaerobic treatment of LCFA-containing feed at 20 °C was shown to be feasible and was linked to the microbial community dynamics in high-rate reactors. During a two-month operation, a soluble COD removal of 84-91% and COD to methane conversion of 44-51% was obtained. However, granular sludge flotation and washout occurred after two months in all reactors without volatile fatty acids (VFA) accumulation, emphasizing the need for sludge retention for long-term granular sludge reactor operation with LCFA-containing feed at low ambient temperatures. The temporal shifts in microbial community structure were studied in the high-rate treatment of SDW, and the process disturbances (elevated LCFA loading, LCFA accumulation, and batch operation) were found to decrease the microbial community diversity. The relative abundance of Methanosaeta increased with higher LCFA accumulation in the settled and flotation layer granules in the three reactors, therefore, acetoclastic methanogenesis was found to be crucial for the high-rate treatment of SDW at 20 °C. This study provides an initial understanding of the continuous anaerobic treatment of LCFA-containing industrial wastewaters at low ambient temperatures.

Spatio-temporal Patterns of Microbial Communities and Their Driving Mechanisms in Subalpine Lakes, Ningwu, Shanxi

Human activities and climate change cause the degradation of subalpine lake ecosystems, which induce the shift of microbial community structure. The spatio-temporal dynamics and the diversity maintenance mechanisms of bacterial communities in Gonghai Lake in Ningwu, Shanxi, were investigated by using Q-PCR and DGGE. The results showed that the temperature), pH, dissolved oxygen, electrical conductivity salinity, and ammonium nitrogen (NH4+) contestation were significantly different among the different sampling depths during different months. Bacterial abundance was the highest in August and the lowest in November, and the abundance was higher in the middle water layer (2 m, 4 m, and 6 m depths), but relatively low in the surface layer and bottom layer (0 m and 8 m depths, respectively). The α diversity index of bacterial communities had significant differences among the different months and depths, and showed an initial decreasing trend and then an increasing trend from April to December. A PERMANOVA test showed that the spatial distribution of bacterial communities was significantly different among depths (P<0.001). The results of redundancy analysis and variation partitioning indicated that environmental selection and diffusion limitation had an effect on the maintenance of the diversity patterns of bacterial communities at the different depths of GH. However, the relative effect of environmental factors was stronger, of which the concentration of NO3-, NO2-, and NH4+ were the main influencing factors. In conclusion, the bacterial communities in GH subalpine lake showed clear spatio-temporal distribution patterns, and environmental variables had a significant effect on shaping the community diversity.

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient.

A majority of environmental studies describe microbiomes at coarse scales of taxonomic resolution (bacterial community, phylum), ignoring key ecological knowledge gained from finer-scales and microbial indicator taxa. Here, we characterized the distribution of 940 bacterial taxa from 41 streams along an urbanization gradient (0%-83% developed watershed area) in the Raleigh-Durham area of North Carolina (USA). Using statistical approaches derived from macro-organismal ecology, we found that more bacterial taxa were classified as intolerant than as tolerant to increasing watershed urbanization (143 vs 48 OTUs), and we identified a threshold of 12.1% developed watershed area beyond which the majority of intolerant taxa were lost from streams. Two bacterial families strongly decreased with urbanization: Acidobacteriaceae (Acidobacteria) and Xanthobacteraceae (Alphaproteobacteria). Tolerant taxa were broadly distributed throughout the bacterial phylogeny, with members of the Comamonadaceae family (Betaproteobacteria) presenting the highest number of tolerant taxa. Shifts in microbial community structure were strongly correlated with a stream biotic index, based on macroinvertebrate composition, suggesting that microbial assemblages could be used to establish biotic criteria for monitoring aquatic ecosystems. In addition, our study shows that classic methods in community ecology can be applied to microbiome datasets to identify reliable microbial indicator taxa and determine the environmental constraints on individual taxa distributions along environmental gradients.

Effect of ammonium to nitrite ratio on reactor performance and microbial population structure in anammox reactors

ABSTRACT Anaerobic ammonium oxidation (anammox) presents an efficient alternative for conventional nitrogen removal process. In this study, the effect of varying Substrate (ammonium to nitrite) ratios on reactor performance and microbial community structures within three anaerobic sequencing batch reactors (ASBRs) was investigated. Three 1 L ASBRs (Reactors 1, 2 and 3) were operated under similar operational conditions. By varying the ammonium to nitrite ratios, a significant variation in nitrogen removal was observed after 170 days of operation: nitrogen removal efficiencies of 67.17 ± 7.29%, 57.13 ± 11.18% and 56.26 ± 17.05% in Reactors 3, 2 and 1 respectively were achieved. Similarly, using quantitative PCR, an overall variation in the population of anammox bacteria, ammonia oxidizing bacteria (AOB), Nitrospira and copy numbers of nirS, hzo and hzs genes were observed with varying degrees of expression. High throughput sequencing analysis further showed a shift in microbial community structure with an overall increase in population of Planctomycetia from 0.76% to (3%, 25% and 26%) and Betaproteobacteria from 5.38% to (19%, 21% and 43%) within Reactors 1, 2 and 3, respectively. In conclusion, different substrates ratio showed a significant influence on the overall nitrogen removal rate as well as the abundances of the different microbial groups.

Magnet anode enhances extracellular electron transfer and enrichment of exoelectrogenic bacteria in bioelectrochemical systems

BackgroundOptimizing the ability of exoelectrogens is a key factor in boosting the overall efficiency of bioelectrochemical systems. In this study, we construct magnetic microbial fuel cells (MFCs) with magnets with different static magnetic field (SMF) intensities for use as anodes. It is proposed as an in situ study of the effects of magnetic fields on the performance and exoelectrogenic biofilm of bioelectrochemical system.ResultsThe magnetic MFCs obtain a 71.0–105% increase in voltage production and a 42.9–104% increase in power density compared with non-magnetic MFCs. MFCs with a MF intensity of 80 mT obtain the best performances. SMF decreases the internal resistance of MFCs, especially its diffusion resistance. The relative abundance of Geobacter in magnetic MFCs is up to 32.5% higher than that of non-magnetic MFC. SMFs also lead to the shifts in microbial community structure of methanogens.ConclusionThe constructed magnetic MFCs obtained better performance compared with the non-magnetic MFC, in terms of voltage production, power density, and coulombic efficiency. The relative abundance of Geobacter spp. (one kind of exoelectrogen) was much higher in the magnetic MFCs. The optimal static magnetic field intensity for enriching exoelectrogens is around 80 mT. It is likely that the decrease of internal resistance, enrichment in exoelectrogens, and the syntrophic interactions between exoelectrogens and methanogens result in the enhanced performance of magnetic MFCs. This study provides a magnetic method for the enrichment of exoelectrogens, which can be extensively applied in bioelectrochemical systems.

Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities.

The Caspian Sea, which is the largest landlocked body of water on the planet, receives substantial annual hydrocarbon input from anthropogenic sources (e.g., industry, agriculture, oil exploration, and extraction) and natural sources (e.g., mud volcanoes and oil seeps). The Caspian Sea also receives substantial amounts of runoff from agricultural and municipal sources, containing nutrients that have caused eutrophication and subsequent hypoxia in the deep, cold waters. The effect of decreasing oxygen saturation and cold temperatures on oil hydrocarbon biodegradation by a microbial community is not well characterized. The purpose of this study was to investigate the effect of oxic and anoxic conditions on oil hydrocarbon biodegradation at cold temperatures by microbial communities derived from the Caspian Sea. Water samples were collected from the Caspian Sea for study in experimental microcosms. Major taxonomic orders observed in the ambient water samples included Flavobacteriales, Actinomycetales, and Oceanospirillales. Microcosms were inoculated with microbial communities from the deepest waters and amended with oil hydrocarbons for 17 days. Hydrocarbon degradation and shifts in microbial community structure were measured. Surprisingly, oil hydrocarbon biodegradation under anoxic conditions exceeded that under oxic conditions; this was particularly evident in the degradation of aromatic hydrocarbons. Important microbial taxa associated with the anoxic microcosms included known oil degraders such as Oceanospirillaceae. This study provides knowledge about the ambient community structure of the Caspian Sea, which serves as an important reference point for future studies. Furthermore, this may be the first report in which anaerobic biodegradation of oil hydrocarbons exceeds aerobic biodegradation.

Interactive carbon priming, microbial response and biochar persistence in a Vertisol with varied inputs of biochar and labile organic matter

There has been great interest in biochar application to soil for long‐term carbon (C) sequestration. However, the interactive priming of organic C mineralization, including shifts in microbial community structure and the persistence of biochar in a clayey soil amended with biochar and labile organic matter (LOM) over a relatively long period (i.e. years) remain poorly understood. A 2‐year incubation study was carried out with δ13C‐depleted biochars produced from Eucalyptus saligna Sm. wood biomass at 450 and 550°C. Each of the biochars (at 2%, w/w) in combination with LOM, such as sugarcane residue at input rates of 0, 1, 2 or 4% w/w, were mixed with a C4‐dominated Vertisol. The interactive effect of biochar and LOM on the structure of the microbial community was analysed by terminal restriction fragment length polymorphism (T‐RFLP). Our results showed that at the small LOM rates (0 and 1%), there was a positive priming effect of biochar on organic C in soil (i.e. native soil organic C (SOC) + LOM‐C)), which shifted to being negative when the LOM input was increased to 2 or 4%. Over the 2 years, mineralization of C from the 450°C biochar (1.2–1.7%) was significantly greater than that for 550°C biochar (0.6–1.0%), and the positively primed mineralization of biochar‐C by LOM was enhanced by the increasing rates of LOM input. The negative priming of native SOC + LOM‐C mineralization by biochar was greater at large than small inputs of LOM, which would have been facilitated by greater shifting in fungal communities, while enhancing biochar‐C mineralization and possibly soil aggregation. In conclusion, over the long term, the amount of LOM stabilized by biochar was greater than that of positively primed biochar‐C mineralization by LOM, in particular at the large LOM input. Biochar can persist in soil on a centennial scale and decreases the turnover of native SOC + LOM‐C over the long term, whereas LOM input can shift microbial communities, favouring LOM stabilization in the biochar‐amended Vertisol.Highlights Do C priming, biochar persistence and microbial response change 2 years after biochar–LOM inputs? Examined interactive C priming (stable‐C isotope), microbial community structure and biochar MRT. Priming of SOC ± LOM‐C by biochar and vice‐versa increased with LOM inputs. Biochar–LOM interaction (2‐year) shifted microorganisms, favouring LOM‐C stabilization in a Vertisol.

Halogenated flame retardants in mangrove sediments from the Pearl River Estuary, South China: Comparison with historical data and correlation with microbial community

Polybrominated diphenyl ethers (PBDEs), decabromodiphenyl ethane (DBDPE), 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE), tetrabromobisphenol A (TBBPA), hexabromocyclododecane (HBCDD) and dechlorane plus (DP) were measured in sediments collected from three mangrove wetlands of the Pearl River Estuary (PRE) in South China. This study aims to investigate the distribution of these halogenated flame retardants (HFRs) and the correlations between HFRs and microbial community structure in mangrove sediments. Concentrations of PBDEs, DBDPE, BTBPE, TBBPA, HBCDD and DP in mangrove sediments ranged from 6.97 to 216.1, 3.70–26.0, 0.02–0.73, 0.02–37.5, 0.44–127.5 and 0.07–2.23 ng/g dry weight, respectively. Higher levels of PBDEs, BTBPE, HBCDD and DP were observed in sediments from Futian mangrove wetland of Shenzhen, the only nature reserve located in the downtown of China. The highest concentration of TBBPA found in mangrove sediments from Guangzhou was proximate to a ferry terminal and a dockyard where TBBPA is widely used in the coatings. PBDEs were the predominant HFRs in mangrove sediments, with an average contribution of 63.0%. Mangrove sediments from Guangzhou and Zhuhai showed an enrichment of (−)-α-HBCDD, (−)-β-HBCDD and (−)-γ-HBCDD. Concentrations of HFRs in mangrove sediments from Guangzhou increased significantly from 2012 to 2015, which was probably due to the establishment and rapid development of Nansha Free Trade Zone of Guangzhou. Redundancy analysis showed that HFRs may cause a shift of microbial community structure in mangrove sediments and the variations were significantly correlated with TBBPA, syn-DP and BTBPE.

High-Alpine Permafrost and Active-Layer Soil Microbiomes Differ in Their Response to Elevated Temperatures.

The response of microbial communities to the predicted rising temperatures in alpine regions might be an important part of the ability of these ecosystems to deal with climate change. Soil microbial communities might be significantly affected by elevated temperatures, which influence the functioning of soils within high-alpine ecosystems. To evaluate the potential of the permafrost microbiome to adapt to short-term moderate and extreme warming, we set up an incubation experiment with permafrost and active soil layers from northern and southern slopes of a high-alpine mountain ridge on Muot da Barba Peider in the Swiss Alps. Soils were acclimated to increasing temperatures (4–40°C) for 26 days before being exposed to a heat shock treatment of 40°C for 4 days. Alpha-diversity in all soils increased slightly under gradual warming, from 4 to 25°C, but then dropped considerably at 40°C. Similarly, heat shock induced strong changes in microbial community structures and functioning in the active layer of soils from both northern and southern slope aspects. In contrast, permafrost soils showed only minor changes in their microbial community structures and no changes in their functioning, except regarding specific respiration activity. Shifts in microbial community structures with increasing temperature were significantly more pronounced for bacteria than for fungi, regardless of the soil origin, suggesting higher resistance of high-alpine fungi to short-term warming. Firmicutes, mainly represented by Tumebacillus and Alicyclobacillaceae OTUs, increased strongly at 40°C in active layer soils, reaching almost 50% of the total abundance. In contrast, Saccharibacteria decreased significantly with increasing temperature across all soil samples. Overall, our study highlights the divergent responses of fungal and bacterial communities to increased temperature. Fungi were highly resistant to increased temperatures compared to bacteria, and permafrost communities showed surprisingly low response to rising temperature. The unique responses were related to both site aspect and soil origin indicating that distinct differences within high-alpine soils may be driven by substrate limitation and legacy effects of soil temperatures at the field site.

Phylogenetic analysis of the key microorganisms shifting in hydrolysis and subsequent fermentation while treating waste activated sludge by thermophilic bacteria

Employment of thermophilic bacteria for the pretreatment of waste activated sludge is one of efficient biological processes, which also benefits further sludge digestion. After pretreatment, volatile fatty acids production in the fermentation process was increased to 2521 ± 24 mg COD/L, which was 43% high compared to the control. The shift of microbial community structure from thermophilic pretreatment to hydrolysis might have substantially affected the subsequent WAS acidification. This study has been focused to investigate the links between community structure and functional genes on WAS hydrolysis and acidification after inoculation of Geobacillus sp. G1. The corresponding quantification of genus Geobacillus and proteolytic genes in WAS were explored. Diverse hydrolysis bacteria with a strong ability to degrade proteins and amino acids were detected. Bacterodies were enriched to utilize hydrolysis organics to directly produce organic acids. WAS hydrolysis was efficiently accelerated through pretreatment and volatile fatty acids production was effectively improved.

Dynamics of microbial community and tetracycline resistance genes in biological nutrient removal process

The occurrence of antibiotics in wastewater has become a serious concern due to the possible development of antibiotic resistant bacteria in wastewater treatment process. In order to understand the dynamics of microbial community and tetracycline resistance genes in biological nutrient removal (BNR) process, three lab-scale sequencing batch reactors (SBRs) were operated under the stress of tetracycline. Results indicated that microbial community structure was altered, and tetracycline efflux pump genes were enhanced over 150-day operation in the presence of trace tetracycline of 20 and 50 μg L−1, respectively. Furthermore, when the initial tetracycline concentrations were increased to 2 and 5 mg L−1, substantial enhancement of tetracycline resistance was observed, accompanied with a sharp shift in microbial community structure. In this study, horizontal gene transfer was found to be the main mechanism for the development of tetracycline resistance genes under the long-terms stress of trace tetracycline. About 90.34% of the observed variations in tetracycline resistance genes could be explained by the dynamics of potential hosts of tetracycline resistance genes and class 1 integron. It should be noticed that the functional bacteria (e.g. Nitrospira, Dechloromonas, Rhodobacter and Candidatus_Accumulibacter) responsible for nutrient removal were positively correlated with tetracycline resistance, which might promote the prevalence of tetracycline resistance during biological wastewater treatment. Consequently, this study provided in-depth insights into the occurrence and prevalence of tetracycline resistance genes and their microbial hosts in BNR process.

Soil Microbial Community Structure Shifts Induced by Biochar and Biochar‐Based Fertilizer Amendment to Karst Calcareous Soil

Core Ideas Biochar‐based fertilizer treatments induced significant microbial community structure shifts compared with no‐biochar and biochar alone. Biochar‐based fertilizer especially at higher biochar addition rate increased soil microbial biomass and fertility. Soil microbial species were strongly correlated with soil nutrients under biochar and biochar‐based fertilizer into karst soil. Karst ecosystems are vulnerable to degradation and constitute a significant proportion of southwestern China. Here, we explore the amendment of these soils with wood biochar in combination with N‐P‐K fertilizer and swine manure compost with the goal of improving microbial community structure and soil nutrient status of these soils. A pot experiment with six treatments, including control (CK, no amendment), swine manure compost plus N‐P‐K fertilizer (MF), wood biochar at 2% in soil (W2), wood biochar at 4% in soil (W4), wood biochar‐based fertilizer at 2% in soil (W2MF), and biochar‐based fertilizer at 4% in soil (W4MF), was set up for 20 months. The results showed that soil organic matter and soil available nutrients N, P, and K in W4MF increased by 63.95, 66.23, 284.96, and 94.56%, respectively, compared with CK. Soil microbial biomass C, N, and P increased in sequence by 60.05, 87.64, and 307.85%, respectively. Soil bacterial and fungal diversity indices (Simpson and Shannon) and richness index (Chao1) were generally higher in biochar‐based fertilizer treatments (W2MF and W4MF) than biochar alone (W2 and W4). The bacterial and fungal community structures of biochar based fertilizer treatments differed from those of biochar amendment alone or control (P &lt; 0.05). Linear discriminant (Effect Size) analysis showed that the bacterial biomarkers of the W2MF + W4MF group were mainly the phylum Acidobacteria and class Alphaproteobacteria, and the fungal biomarkers were the phylum Rozellomycota and Glomeromycota. Redundancy analysis revealed strong relationships between microbial community structure and soil organic matter and soil available nutrients N, P, and K (P &lt; 0.05). In conclusion, either sole biochar or biochar‐based fertilizer amendment improved karst soil nutrient conditions and induced microbial community structural shifts. The performance was better in biochar‐based fertilizer treatment than that in biochar addition alone.

Structural and physiological adaptations of soil microorganisms to freezing revealed by position-specific labeling and compound-specific 13C analysis

Psychrotolerant microbes are crucial for carbon cycling and biotechnological applications. Nonetheless, the mechanisms enabling their survival and functioning in frozen environments remain unclear. To elucidate adaptations of microbial cell membranes to freezing, we incubated soils with position-specific 13C labeled glucose at + 5 (control), − 5 and − 20 °C and quantified 13C in CO2 and phospholipid fatty acids. High oxidation of glucose C-1 at + 5 °C revealed a transformation via the pentose phosphate pathway. At subzero temperatures, however, the preferential oxidation of C-4 position suggested a switch to glycolysis. The threefold increase of Gram-negative phospholipid fatty acids in soil incubated at − 5 °C was accompanied by a twofold increase in 13C incorporation. This unequal increase of phospholipid fatty acids and incorporated 13C can be explained by simultaneous desaturation of existing fatty acid chains and the de novo synthesis of monounsaturated fatty acids, which indicates microbial growth. In contrast, Gram-positive bacteria incorporated 2 times higher 13C into their phospholipid fatty acids at − 20 °C than at − 5 and + 5 °C without a significant increase in their fatty acid contents. This reflects intensive repair of membranes damaged at − 20 °C without microbial growth. The fungal/bacterial ratio was 1.5 times lower at subzero temperatures than at + 5 °C, reflecting a shift in microbial community structure towards bacteria. Accordingly, soil microorganisms adapted to freezing by (1) switching their metabolic pathway from the pentose phosphate pathway to glycolysis, (2) modifying phospholipid fatty acids by desaturation and, (3) shifting microbial community structure towards Gram-negative bacteria by reducing the fungal population.

Biochar as a management tool for soilborne diseases affecting early stage nursery seedling production

Biochar is thought to have great potential as a supplemental amendment in nursery growing media. The knowledge of how to optimize the use of biochar in the nursery setting during the most vulnerable pre-emergence and early seedling stages of the plant, however, is underdeveloped. The current study involves pre-emergence trials in the Pythium aphanidermatum-cucumber pathosystem using a commercial nursery potting mixture amended with up to 3% w:w wood-derived biochar. The major questions were: (i) is pre-conditioning required to elicit suppression of pre-emergence damping-off disease in the Pythium-cucumber system; (ii) what are the changes in bacterial community composition and diversity due to pre-conditioning of the biochar-amended potting medium; and (iii) can the pre-conditioning stage be shortened from 45 days and still provide disease suppression. Pre-conditioning, consisting of pre-planting fertigation of the nursery medium, was found to be needed to achieve suppression of damping-off disease by biochar, with a reduction in pre-emergence damping-off caused by P. aphanidermatum by up to 71%. Illumina sequencing of 16s bacterial gene revealed a significant enrichment in the abundance of bacteria in general and potentially beneficial microorganisms in particular, as well as shifts in microbial community structure as a result of biochar addition. These changes may play an important role in the overall effects of biochar on disease suppression in young seedlings. A pre-conditioning period of only 14 days was found to be effective for disease suppression, which can substantially improve its practical utility for nurseries.

Microbial Community Structure Shift During Bioremediation of Petroleum Contaminated Soil Using High Throughput Sequencing

The shift in microbial community structure during the bioremediation of oil-polluted soil was analyzed by high-throughput sequencing. The results demonstrated obvious changes in the soil microbial community structure and diversity during bioremediation. The species richness and evenness of the microbial community decreased substantially due to the bioaugmentation treatment. Proteobacteria became the predominant phylum, with a relative increase in abundance from 37.44% to 87.44%. Pseudomonas was the most dominant genus, which increased in abundance from 2.99% to 76.37%. In the biostimulation treated soil, the relative abundance of Proteobacteria decreased from 37.44% to 10.90%, while the phylum Firmicutes increased from 9.16% to 35.32%. At the genus level, the relative abundances of Exiguobacterium and Promicromonospora decreased from 8.49% and 18.96% to 2.19% and 14.97%, respectively. Nocardioides and Bacillus became the dominant genera and increased from 5.56% and 0.29% to 28.95% and 22.70%, respectively. The results indicated that bioaugmentation substantially influenced the soil microbial diversity and community structure. Additionally, the biostimulation treatment maintained the balance in the soil microbial community structure. The stabilization of bacteria community structure is beneficial to petroleum biodegradation in the soil.

Typology of extreme flood event leads to differential impacts on soil functioning

Soils around the world are being exposed to weather events which are unprecedented in recent history. To maintain the delivery of soil-related ecosystem services and to promote greater soil resilience it is essential to understand how plant-soil systems respond to these extreme events. In this study we replicated a recent period of extreme rainfall and prolonged spring flooding in a temperate grassland which had no previous history of flooding. Intact soil mesocosms (Eutric Cambisol) 1 kg weight were subjected to a simulated long-term spring flood (15 °C, 2 months) and maintained in the light with above ground indigenous vegetation (Lolium perenne L.) or dark with and without indigenous vegetation to simulate different flood typologies. In comparison to a no-flood control treatment, nutrient cycling, water quality, air quality (greenhouse gas emissions), habitat provision and biological population regulation shifts were evaluated. Flooding induced a rapid release of nutrients into the soil solution and overlying floodwater, resulting in potential nutrient losses up to 15 mg Fe, 16 mg NH4+, 360 mg DOC and 28 mg DON, per mesocosm. The presence of plants increased the rate of nutrient release (especially P), with the effects magnified when light transmission through the floodwater was restricted (1.3 mg P vs 0.2 mg P, per mesocosm). Flooding induced a rapid decline in redox potential and subsequent production of CH4, especially in the darkened treatments (10 and between 11 and 16 times higher than the control, without and with light restrictions, respectively). Upon removal of the floodwater, the accumulated NH4+ was nitrified leading to a shift in greenhouse gas emissions, from CH4 to N2O emissions. N2O was only significantly produced in the mesocosms kept under light restrictions (13 times higher than in other two treatments). Flooding eliminated earthworms, reduced grass production after soil recovery (from 28 g for control mesocosms to 11 g and <1 g for flooded mesocosms without and with light restrictions, respectively). Soil microbial biomass was also reduced (up to a 22–27% of the total PLFAs) and flooding induced shifts in microbial community structure, particularly a loss of soil fungi. The soil fungi content quickly recovered (4 weeks) when light was not restricted during the flood period, however, no such recovery was seen in the darkened treatments. Overall, we conclude that extreme flood events cause rapid and profound changes in soil function. Both the impact of the flooding and the time to recover is exacerbated when light is restricted (e.g. in sediment laden floodwater). In addition, our results suggest that the presence of flood-resilient plants can mitigate against some of the negative impacts of flooding on soil functioning.

The ratio of Gram-positive to Gram-negative bacterial PLFA markers as an indicator of carbon availability in organic soils

Despite recent progress in understanding soil microbial responses to carbon (C) limitation, the functional shifts in microbial community structure associated with decreasing soil C availability and changes in organic matter chemistry remain poorly known. It has been proposed that Gram-negative (GN) bacteria use more plant-derived C sources that are relatively labile, while Gram-positive (GP) bacteria use C sources derived from soil organic matter that are more recalcitrant. Because these two groups may differ in how they influence the fate of different C forms in soils, it is important to understand how they vary across ecosystems that differ in their vegetation cover and ecosystem productivity or across environmental gradients. In this study, we used a 19-year plant functional group removal experiment across a long term post-fire chronosequence to assess how microbial community structure (assessed using phospholipids fatty acids; PLFAs) and the association of bacterial functional groups (specifically, the GP:GN ratio) responded to changes in organic matter chemistry (measured via nuclear magnetic resonance; NMR). We found that the GP:GN ratio increased upon removal of shrubs and tree roots and with decreasing ecosystem productivity along the chronosequence, thus showing the greater dependence of GN than GP bacteria on more labile plant-derived C. Overall, GN bacteria were associated with simple C compounds (alkyls) whereas GP bacteria were more strongly associated with more complex C forms (carbonyls). Therefore, we conclude that the GP:GN ratio has potential as a useful indicator of the relative C availability for soil bacterial communities in organic soils, and can be used as a coarse indicator of energy limitation in natural ecosystems.

Combined effects of maize straw biochar and oxalic acid on the dissipation of polycyclic aromatic hydrocarbons and microbial community structures in soil: A mechanistic study.

Whether the rhizodegradation of organic contaminants occurs in biochar- amended soil and its potential mechanisms have rarely been reported. Therefore, a study was conducted to investigate the combined effects of root exudates and biochar on the dissipation of polycyclic aromatic hydrocarbons (PAHs) and on the microbial community structures in soil. As a major component of the root exudates of ryegrass, oxalic acid (OA) significantly enhanced the dissipation of high- and low-ring PAHs in the studied soil with or without maize straw biochar amendment (p < 0.05). However, biochar alone enhanced only the dissipation of high-ring PAHs. The activities of three enzymes (urease, polyphenol oxidase and dehydrogenase) were the highest in soil amended with both maize straw biochar and 0.5 mg kg-1 of OA. Moreover, soil microbial biomass and the abundances of genera and genes associated with PAH degradation were significantly enhanced with the tandem application of biochar and OA (p < 0.05). These changes led to a synergetic effect of biochar and OA on the shifts in microbial community structures and on the dissipation of PAHs, especially for high-ring PAHs. The results in this study suggested that a combined biochar-rhizosphere approach should be a feasible remediation strategy for PAH-contaminated soil.

Host Developmental Toxicity of BPA and BPA Alternatives Is Inversely Related to Microbiota Disruption in Zebrafish

Host-associated microbiota can biotransform xenobiotics, mediate health effects of chemical exposure, and play important roles in early development. Bisphenol A (BPA) is a widespread environmental chemical that has been associated with adverse endocrine and neurodevelopmental effects, some of which may be mediated by microbiota. Growing public concern over the safety of BPA has resulted in its replacement with structurally similar alternatives. In this study, we evaluated whether BPA and BPA alternatives alter microbiota and modulate secondary adverse behavioral effects in zebrafish. Zebrafish were developmentally exposed to BPA, Bisphenol AF (BPAF), Bisphenol B (BPB), Bisphenol F (BPF), or Bisphenol S (BPS). At 10 days post fertilization (dpf), toxicity assessments were completed and 16S rRNA gene sequencing was performed to evaluate potential chemical-dependent shifts in microbial community structure and predicted function. A standard light/dark behavioral assay was used to assess locomotor activity. Based on developmental toxicity assessments at 10 dpf, a range of potencies was observed: BPAF > BPB > BPF ∼ BPA > BPS. Analysis of 16S rRNA gene sequencing data showed significant concentration-dependent disruption of microbial community structure and enrichment of putative microbial functions with exposure to BPS, BPA, or BPF, but not BPB or BPAF. Interestingly, microbial disruption was inversely related to host developmental toxicity and estrogenicity. Exposure to BP analogs did not cause behavioral effects at 10 dpf. Our findings indicate that some BP analogs disrupt host microbiota early in life and demonstrate novel chemical-microbiota interactions that may add important context to current hazard identification strategies.