Heterotrophic Microbial Activity Research Articles

Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant.

Oil spills are a frequent perturbation to the marine environment that has rapid and significant impacts on the local microbiome. Previous studies have shown that exposure to synthetic dispersant alone did not enhance heterotrophic microbial activity or oxidation rates of specific hydrocarbon components but increased the abundance of some taxa (e.g., Colwellia). In contrast, exposure to oil, but not dispersants, increased the abundance of other taxa (e.g., Marinobacter) and stimulated hydrocarbon oxidation rates. Here, we advance these findings by interpreting metatranscriptomic data from this experiment to explore how and why specific components of the microbial community responded to distinct organic carbon exposure regimes. Dispersant alone was selected for a unique community and for dominant organisms that reflected treatment- and time-dependent responses. Dispersant amendment also led to diverging functional profiles among the different treatments. Similarly, oil alone was selected for a community that was distinct from treatments amended with dispersants. The presence of oil and dispersants with added nutrients led to substantial differences in microbial responses, likely suggesting increased fitness driven by the presence of additional inorganic nutrients. The oil-only additions led to a marked increase in the expression of phages, prophages, transposable elements, and plasmids (PPTEPs), suggesting that aspects of microbial community response to oil are driven by the "mobilome," potentially through viral-associated regulation of metabolic pathways in ciliates and flagellates that would otherwise throttle the microbial community through grazing.IMPORTANCEMicrocosm experiments simulated the April 2010 Deepwater Horizon oil spill by applying oil and synthetic dispersants (Corexit EC9500A and EC9527A) to deep ocean water samples. The exposure regime revealed severe negative alterations in the treatments' heterotrophic microbial activity and hydrocarbon oxidation rates. We expanded these findings by exploring metatranscriptomic signatures of the microbial communities during the chemical amendments in the microcosm experiments. Here we report how dominant organisms were uniquely associated with treatment- and time-dependent trajectories during the exposure regimes; nutrient availability was a significant factor in driving changes in metatranscriptomic responses. Remarkable signals associated with PPTEPs showed the potential role of mobilome and viral-associated survival responses. These insights underscore the time-dependent environmental perturbations of fragile marine environments under oil and anthropogenic stress.

Millimetre-scale biomarker heterogeneity in lacustrine shale identifies the nature of signal-averaging and demonstrates anaerobic respiration control on organic matter preservation and dolomitization

Mm-scale and/or µm-scale in situ inorganic geochemical analyses of organic-rich, laminated fine-grained sediments increasingly offer decadal or even seasonal perspectives of ecological or environmental dynamics. Organic geochemical studies, in contrast, seldom explicitly consider mm-scale variability, so that it remains unclear to what extent organic geochemical proxy-based reconstructions are a product of signal-averaging of higher-resolution variability. Here we assess the 2–8 mm-scale variability in organic geochemical proxies for depositional environment and organic source, utilising an organic-rich, low maturity and well-laminated shale from the Eocene Shahejie Formation, Dongying Depression, Bohai Bay Basin. We identify mm-scale (approximately decadal-scale) compositional variability that is comparable in magnitude to vertical variability at the m-scale (approximately millennial-scale), test multiple relationships between key biomarker and mineral proxies at the mm-scale, and assess likely implications for palaeowater conditions, anaerobic heterotrophic microbial activity, early diagenetic dolomitization, and organic matter preservation. Our results suggest that the decadal-scale oscillation of organic carbon content is a result of varying degrees of anaerobic heterotrophic microbial reworking with periodic euxinia in the deep photic zone. In contrast to previous models based on analysis of bulk samples, our results suggest that anaerobic respiration during intervals of more intense/persistent euxinia is likely accompanied by more organic matter loss. Variable low-light euxinia seems to be a modifier to the net OM content. The analysis of bulk samples may hide important relationships at shorter temporal scales which are key to reconstructing palaeoenvironments and the operation of key controls on, for example, the carbon cycle.

Groundwater‐stream connections shape the spatial pattern and rates of aquatic metabolism

AbstractA longstanding challenge in stream ecology is to understand how landscape configuration organizes spatial patterns of ecosystem function via lateral groundwater connections. We combined laboratory bioassays and field additions of a metabolic tracer (resazurin) to test how groundwater‐stream confluences, or “discrete riparian inflow points” (DRIPs), regulate heterotrophic microbial activity along a boreal stream. We hypothesized that DRIPs shape spatial patterns and rates of aquatic heterotrophic microbial activity by supplying labile dissolved organic matter (DOM) to streams. Laboratory bioassays showed that the potential influence of DRIPs on heterotrophic activity varied spatially and temporally, and was related to their DOM content and composition. At the reach scale, DRIP‐stream confluences elevated the spatial heterogeneity and whole‐reach rates of heterotrophic activity, especially during periods of high land–water hydrological connectivity. Collectively, our results show how the arrangement of lateral groundwater connections influence heterotrophic activity in streams with implications for watershed biogeochemical cycles.

A device for assessing microbial activity under ambient hydrostatic pressure: The in situ microbial incubator (ISMI).

Microbes in the dark ocean are exposed to hydrostatic pressure increasing with depth. Activity rate measurements and biomass production of dark ocean microbes are, however, almost exclusively performed under atmospheric pressure conditions due to technical constraints of sampling equipment maintaining in situ pressure conditions. To evaluate the microbial activity under in situ hydrostatic pressure, we designed and thoroughly tested an in situ microbial incubator (ISMI). The ISMI allows autonomously collecting and incubating seawater at depth, injection of substrate and fixation of the samples after a preprogramed incubation time. The performance of the ISMI was tested in a high-pressure tank and in several field campaigns under ambient hydrostatic pressure by measuring prokaryotic bulk 3H-leucine incorporation rates. Overall, prokaryotic leucine incorporation rates were lower at in situ pressure conditions than under to depressurized conditions reaching only about 50% of the heterotrophic microbial activity measured under depressurized conditions in bathypelagic waters in the North Atlantic Ocean off the northwestern Iberian Peninsula. Our results show that the ISMI is a valuable tool to reliably determine the metabolic activity of deep-sea microbes at in situ hydrostatic pressure conditions. Hence, we advocate that deep-sea biogeochemical and microbial rate measurements should be performed under in situ pressure conditions to obtain a more realistic view on deep-sea biotic processes.

Eddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North Atlantic

Abstract. Mesoscale eddies modulate the ocean's physical, chemical, and biological properties. In cyclonic eddies (CEs), nutrient upwelling can stimulate primary production by phytoplankton. Yet, how this locally enhanced autotrophic production affects heterotrophy and consequently the metabolic balance between the synthesis and the consumption of dissolved organic matter (DOM) remains largely unknown. To fill this gap, we investigated the horizontal and vertical variability in auto- and heterotrophic microbial activity (biomass production and respiration) within a CE that formed off Mauritania and along the ∼ 900 km zonal corridor between Mauritania and the Cape Verde islands in the Eastern Tropical North Atlantic (ETNA). Our results show how the physical disturbances caused by the CE affected the biomass distribution of phyto- and bacterioplankton and their metabolic activities. The injection of nutrients into the sunlit surface resulted in enhanced autotrophic pico- and nanoplankton abundance and generally increased autotrophic activity as indicated by chlorophyll a (Chl a) concentration, primary production (PP), and extracellular release rates. However, the detailed eddy survey also revealed an uneven distribution of these variables with, for example, the highest Chl a concentrations and PP rates occurring near and just beyond the CE's periphery. The heterotrophic bacterial activity was similarly variable. Optode-based community respiration (CR), bacterial respiration (BR) estimates, and bacterial biomass production (BP) largely followed the trends of PP and Chl a. Thus, a submesoscale spatial mosaic of heterotrophic bacterial abundance and activities occurred within the CE that was closely related to variability in autotrophic production. Consistent with this, we found a significant positive correlation between concentrations of semi-labile dissolved organic carbon (SL-DOC; here the sum of dissolved hydrolysable amino acids and dissolved combined carbohydrates) and BR estimates. Extracellular release of carbon as indicated by primary production of dissolved organic carbon (PPDOC) was variable with depth and laterally and not always sufficient to compensate the bacterial carbon demand (BCD: BR + BP), with PPDOC accounting for between 28 % and 110 % of the BCD. Bacterial growth efficiency (BGE: BP / BCD) ranged between 1.7 % and 18.2 %. We estimated the metabolic state to establish whether the CE was a source or a sink of organic carbon. We showed that the CE carried a strong autotrophic signal in the core (PP / CR > 1). Our results suggest that submesoscale (0–10 km) processes lead to highly variable metabolic activities in both photoautotrophic and heterotrophic microorganisms. Overall, we revealed that the CEs not only trap and transport coastal nutrients and organic carbon to the open ocean but also stimulate phytoplankton growth, generating freshly produced organic matter during westward propagation. This drives heterotrophic processes and may contribute to the previously observed net heterotrophy in open Atlantic surface waters.

Patterns of microbial abundance and heterotrophic activity along nitrogen and salinity gradients in coastal wetlands

Coastal wetlands are valuable aquatic ecosystems with high biological productivity, which provide services such as a reduction in nitrogen loading into coastal waters and storage of organic carbon acting as carbon dioxide sinks. The predicted rise of sea level or freshwater extractions, particularly in the arid Mediterranean biome, will salinize many coastal wetlands. However, there is considerable uncertainty about how salinization will affect microbial communities and biogeochemical processes. We determined the abundance of total prokaryotes, cyanobacteria, and viruses and quantified the heterotrophic production of prokaryotes sensitive- (predominantly Bacteria) and resistant- (predominantly Archaea) to erythromycin in 112 ponds from nine coastal wetlands. We explored the main drivers of prokaryotic abundance and heterotrophic production using generalized linear models (GLMs). The best GLM, including all the wetlands, indicated that the concentration of total dissolved nitrogen (TDN) positively affected the total abundance of prokaryotes and the heterotrophic erythromycin-resistant (ery-R) production. In contrast, heterotrophic erythromycin-sensitive (ery-S) production was negatively related to TDN. This negative relationship appeared to be mediated by salinity and virus abundance. Heterotrophic ery-S production declined as salinity and virus abundance increased. Consequently, we observed a switch from heterotrophic ery-S production towards ery-R production as salinity and virus abundance increased. Our results imply that microbial activity will change from heterotrophic bacterial-dominated processes to archaeal-dominated processes with anthropogenic nitrogen and salinization increases. However, more studies are required to link the mineralization rates of dissolved nitrogen and organic carbon with specific archaeal taxa to enable more accurate predictions on future scenarios in coastal wetlands.

Quantifying the influence of different biocrust community states and their responses to warming temperatures on soil biogeochemistry in field and mesocosm studies

Biocrusts influence soil biogeochemistry by fixing carbon (C) and nitrogen (N) and through leachate inputs to soils. Functional rates can vary among biocrust community states and in response to edaphic properties, heterotrophic microbial activity, and global change. Using soils and biocrusts from the Colorado Plateau, Utah, USA, we aimed to quantify the influence of early-successional (ES) and late-successional (LS) biocrust community states on soil biogeochemistry. In a field setting, we found soil was less “fertile” under ES than LS biocrust, but ES biocrust had a relative influence 1.3 times greater than LS biocrust on soil fertility. Leachate collected from LS biocrust had, on average, 6 times more organic C and 1.7 times more dissolved N than ES biocrust, but concentrations of phosphorus (P) and inorganic N did not differ among the two biocrust types. To disentangle influences of biocrusts and soil properties on biogeochemical pools, we constructed mesocosms from homogenized soil and left the surface bare or covered with ES or LS biocrust, before assignment to ambient or warmed (+5 °C) temperature treatments for 3 months. Multivariate biogeochemical properties differed among cover types, yet all exhibited losses of P, N, and organic C and nearly half of the biogeochemical variables considered did not differ among cover types. Mesocosms with LS biocrust retained more dissolved N, supported 8 additional, significant correlations among biogeochemical pools of the biocrust and mineral soil layer on average, and lost fewer of these correlations under warming. Overall, while soils under LS biocrusts were more fertile (i.e., had higher nutrient concentrations) than under ES, we did not find evidence implicating leachate as the primary driver of this difference. Biocrust influences on soil fertility were greater when mineral soil nutrients were in lower concentrations, highlighting the value of even incipient biocrusts for dryland functioning.

Empirical leucine-to-carbon conversion factors in north-eastern Atlantic waters (50\u20132000\xa0m) shaped by bacterial community composition and optical signature of DOM

Microbial heterotrophic activity is a major process regulating the flux of dissolved organic matter (DOM) in the ocean, while the characteristics of this DOM strongly influence its microbial utilization and fate in the ocean. In order to broaden the vertical resolution of leucine-to-carbon conversion factors (CFs), needed for converting substrate incorporation into biomass production by heterotrophic bacteria, 20 dilution experiments were performed in the North Atlantic Ocean. We found a depth-stratification in empirical CFs values from epipelagic to bathypelagic waters (4.00 ± 1.09 to 0.10 ± 0.00 kg C mol Leu−1). Our results demonstrated that the customarily used theoretical CF of 1.55 kg C mol Leu−1 in oceanic samples can lead to an underestimation of prokaryotic heterotrophic production in epi- and mesopelagic waters, while it can overestimate it in the bathypelagic ocean. Pearson correlations showed that CFs were related not only to hydrographic variables such as temperature, but also to specific phylogenetic groups and DOM quality and quantity indices. Furthermore, a multiple linear regression model predicting CFs from relatively simple hydrographic and optical spectroscopic measurements was attempted. Taken together, our results suggest that differences in CFs throughout the water column are significantly connected to DOM, and also reflect differences linked to specific prokaryotic groups.

Contrasting Effects of Environmental Concentrations of Sulfonamides on Microbial Heterotrophic Activities in Freshwater Sediments.

The sulfonamide antibiotics sulfamethoxazole (SMX) and sulfamethazine (SMZ) are regularly detected in surface sediments of contaminated hydrosystems, with maximum concentrations that can reach tens of μg kg–1 in stream and river sediments. Little is known about the resulting effects on the exposed benthic organisms. Here we investigated the functional response of stream sediment microbial communities exposed for 4 weeks to two levels of environmentally relevant concentrations of SMX and SMZ, tested individually. To this end, we developed a laboratory channel experiment where natural stream sediments were immersed in water contaminated with nominal environmental concentrations of 500 and 5,000 ng L–1 of SMX or SMZ, causing their accumulation in surface sediments. The mean maximum concentrations measured in the sediment (about 2.1 μg SMX kg–1 dw and 4.5 μg SMZ kg–1 dw) were consistent with those reported in contaminated rivers. The resulting chronic exposure had various effects on the functional potential of the sediment microbial communities, according to the substance (SMX or SMZ), the type of treatment (high or low) and the measured activity, with a strong influence of temporal dynamics. Whereas the SMZ treatments resulted in only transient effects on the five microbial activities investigated, we observed a significant stimulation of the β-glucosidase activity over the 28 days in the communities exposed to the high concentration of SMX. Together with the stimulation of aerobic respiration at low SMX concentrations and the reduced concentration observed in the last days, our results suggest a potential biodegradation of sulfonamides by microbial communities from sediments. Given the key functional role of surface sediment microbial communities in streams and rivers, our findings suggest that the frequently reported contamination of sediments by sulfonamides is likely to affect biogeochemical cycles, with possible impact on ecosystem functioning.

Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters.

Rivers connect the carbon cycle in land with that in aquatic ecosystems by transporting and transforming terrestrial organic matter (TeOM). The Amazon River receives huge loads of TeOM from the surrounding rainforest, promoting a substantial microbial heterotrophic activity and consequently, CO2 outgassing. In the Amazon River, microbes degrade up to 55% of the lignin present in the TeOM. Yet, the main microbial genomes involved in TeOM degradation were unknown. Here, we characterize 51 population genomes (PGs) representing some of the most abundant microbes in the Amazon River deriving from 106 metagenomes. The 51 reconstructed PGs are among the most abundant microbes in the Amazon River, and 53% of them are not able to degrade TeOM. Among the PGs capable of degrading TeOM, 20% were exclusively cellulolytic, while the others could also oxidize lignin. The transport and consumption of lignin oxidation byproducts seemed to be decoupled from the oxidation process, being apparently performed by different groups of microorganisms. By connecting the genomic features of abundant microbes in the Amazon River with the degradation machinery of TeOM, we suggest that a complex microbial consortium could explain the quick turnover of TeOM previously observed in this ecosystem.

Overlooked Implication of Sediment Transport at Low Flow: Migrating Ripples Modulate Streambed Phototrophic and Heterotrophic Microbial Activity

AbstractSandy streambeds are mobile even at low flow velocities at which sediments can be transported as bedload, more specifically as migrating ripples. Small variations in discharge can result in transitions between sediment transport and no‐transport. Despite being inherent processes of streams and rivers, the effect of sediment transport and transport regime transition on the phototrophic and heterotrophic activity of streambed microbial communities remains unclear. We performed a microcosm experiment mimicking sediment transport as migrating ripples (i.e., migrating) and no sediment transport (i.e., stationary), and their transition to observe the response of the phototrophic and heterotrophic microbial community. Both net community production and community respiration were respectively 77% and 40% suppressed in migrating sediments compared to stationary sediments. In migrating sediments, a combination of mechanical stress, light limitation, and limited habitable area likely hampered microbial metabolism. Stationary conditions facilitated an active community of phototrophs, mainly diatoms, as indicated by high net community production, high rates of dissolved organic carbon release and silicon retention. After transitioning migrating to stationary and vice versa, differences were maintained regardless of the change in mechanical stress and associated stressors, most likely as a result of the interaction between their antecedent transport conditions and developmental stage that shaped the microbial community. Our results indicate that sediment transported as migrating ripples at low flow velocity can strongly modulate streambed metabolism, and discharge oscillations resulting in sediment transport transitions will result in a mosaic of microbial activity and biomass that will emerge at larger scales determining reach‐scale metabolism.

Adsorption of titanium dioxide nanoparticles onto zebrafish eggs affects colonizing microbiota

Teleost fish embryos are protected by two acellular membranes against particulate pollutants that are present in the water column. These membranes provide an effective barrier preventing particle uptake. In this study, we tested the hypothesis that the adsorption of antimicrobial titanium dioxide nanoparticles onto zebrafish eggs nevertheless harms the developing embryo by disturbing early microbial colonization. Zebrafish eggs were exposed during their first day of development to 2, 5 and 10 mg TiO2 L−1 (NM-105). Additionally, eggs were exposed to gold nanorods to assess the effectiveness of the eggs’ membranes in preventing particle uptake, localizing these particles by way of two-photon microscopy. This confirmed that particles accumulate onto zebrafish eggs, without any detectable amounts of particles crossing the protective membranes. By way of particle-induced X-ray emission analysis, we inferred that the titanium dioxide particles could cover 25–45 % of the zebrafish egg surface, where the concentrations of sorbed titanium correlated positively with concentrations of potassium and correlated negatively with concentrations of silicon. A combination of imaging and culture-based microbial identification techniques revealed that the adsorbed particles exerted antimicrobial effects, but resulted in an overall increase of microbial abundance, without any change in heterotrophic microbial activity, as inferred based on carbon substrate utilization. This effect persisted upon hatching, since larvae from particle-exposed eggs still comprised higher microbial abundance than larvae that hatched from control eggs. Notably, pathogenic aeromonads tolerated the antimicrobial properties of the nanoparticles. Overall, our results show that the adsorption of suspended antimicrobial nanoparticles on aquatic eggs can have cascading effects across different life stages of oviparous animals. Our study furthermore suggests that aggregation dynamics may occur that could facilitate the dispersal of pathogenic bacteria through aquatic ecosystems.

Evidence That Microorganisms at the Animal-Water Interface Drive Sea Star Wasting Disease.

Sea star wasting (SSW) disease describes a condition affecting asteroids that resulted in significant Northeastern Pacific population decline following a mass mortality event in 2013. The etiology of SSW is unresolved. We hypothesized that SSW is a sequela of microbial organic matter remineralization near respiratory surfaces, one consequence of which may be limited O2 availability at the animal-water interface. Microbial assemblages inhabiting tissues and at the asteroid-water interface bore signatures of copiotroph proliferation before SSW onset, followed by the appearance of putatively facultative and strictly anaerobic taxa at the time of lesion genesis and as animals died. SSW lesions were induced in Pisaster ochraceus by enrichment with a variety of organic matter (OM) sources. These results together illustrate that depleted O2 conditions at the animal-water interface may be established by heterotrophic microbial activity in response to organic matter loading. SSW was also induced by modestly (∼39%) depleted O2 conditions in aquaria, suggesting that small perturbations in dissolved O2 may exacerbate the condition. SSW susceptibility between species was significantly and positively correlated with surface rugosity, a key determinant of diffusive boundary layer thickness. Tissues of SSW-affected individuals collected in 2013–2014 bore δ15N signatures reflecting anaerobic processes, which suggests that this phenomenon may have affected asteroids during mass mortality at the time. The impacts of enhanced microbial activity and subsequent O2 diffusion limitation may be more pronounced under higher temperatures due to lower O2 solubility, in more rugose asteroid species due to restricted hydrodynamic flow, and in larger specimens due to their lower surface area to volume ratios which affects diffusive respiratory potential.

The effects of decomposing invasive jellyfish on biogeochemical fluxes and microbial dynamics in an ultra-oligotrophic sea

Abstract. Over the past several decades, jellyfish blooms have intensified spatially and temporally, affecting functions and services of ecosystems worldwide. At the demise of a bloom, an enormous amount of jellyfish biomass sinks to the seabed and decomposes. This process entails reciprocal microbial and biogeochemical changes, typically enriching the water column and seabed with large amounts of organic and inorganic nutrients. Jellyfish decomposition was hypothesized to be particularly important in nutrient-impoverished ecosystems, such as the Eastern Mediterranean Sea – one of the most oligotrophic marine regions in the world. Since the 1970s, this region has been experiencing the proliferation of a notorious invasive scyphozoan jellyfish, Rhopilema nomadica. In this study, we estimated the short-term decomposition effects of R. nomadica on nutrient dynamics at the sediment–water interface. Our results show that the degradation of R. nomadica has led to increased oxygen demand and acidification of overlying water as well as high rates of dissolved organic nitrogen and phosphate production. These conditions favored heterotrophic microbial activity and bacterial biomass accumulation, and triggered a shift towards heterotrophic biodegrading bacterial communities, whereas autotrophic picophytoplankton abundance was moderately affected or reduced. This shift may further decrease primary production in the water column of the Eastern Mediterranean Sea. Deoxygenation, acidification, nutrient enrichment, and microbial community shifts at the sediment–water interface may have a detrimental impact on macrobenthic communities. Based on these findings, we suggest that jelly-falls and their decay may facilitate an additional decline in ecosystem functions and services.

The effect of climate warming on microbial loop function in peat pools and Sphagnum hollows: Mesocosm experiments

AbstractClimate change models predict a possible increase in air temperature of 2–8°C. This means that global warming will significantly affect the functioning of various types of hydrogenic ecosystems. However, the effect of the temperature increase on microbial loop function in small water bodies associated with peat ecosystems (peat pools and Sphagnum hollows) is still unknown. We used mesocosm experiments (control and treatments with a 2°C, 4°C and 8°C temperature increase) to determine the response of bacterioplankton, flagellates, testate amoebae and ciliates to simulated temperature changes, taking into account seasonal variation in the temperate climate zone. The simulated increase in climate warming increased the species richness of ciliates and the abundance of bacteria, flagellates and ciliates. In contrast, there was a decrease in the species number and abundance of testate amoebae, the top predators in peat ecosystems. The sensitivity of the various microbial groups to temperature was size‐dependent; large‐sized testate amoebae declined under warming. These shifts caused a decrease in the predator–prey mass ratio. An increase in the abundance of top predators promotes increased abundance of ciliates, and thus changes the architecture of the food web. At the same time, we observed the increase in phycoflora biomass thus can cancel the potential negative effects of warming on heterotrophic microbial activity. So, the potential effect of warming on the C budgets of peat pools and hollows is evident. A better understanding of what regulates microbial populations and activity in small reservoirs in peat bogs and unravelling of these fundamental mechanisms are particularly critical to more accurately predict how peat bogs will respond to climate disturbances.

Pasture in crop rotations influences microbial biodiversity and function reducing the potential for nitrogen loss from compost

Agroecosystems make up a significant portion of terrestrial ecosystems and receive a disproportionally high amount of terrestrial nitrogen inputs from fertilizer, leading to nitrogen loss and associated environmental problems. Integrated crop livestock systems, such as pasture-integrated crop rotations, may be more environmentally sustainable however the long-term effects of this management practice on soil microorganisms and nitrogen transformations are not well understood. To address this knowledge gap, samples were collected from a long-term experiment designed to assess the impacts of, and interaction between, compost application and pasture-integrated crop rotations. The compost-input and pasture-integrated rotation treatments increased soil organic matter by 41 % and 14 % respectively, carbon mineralization by 127 % and 146 %, and extracellular enzyme activity by 74 % and 35 %, suggesting enhanced heterotrophic microbial activity. Compost addition led to rapid ammonification, increased potential nitrification rates ∼3-fold, and enhanced nitrate concentration by ∼75%. Further, compost addition more than doubled the abundance of prokaryotic ammonia oxidizing organisms (AOO). These effects of compost on nitrogen cycling were greatly mitigated by the pasture-integration likely due to enhanced microbial decomposition activity associated with carbon inputs from perennial grasses. Specifically, pasture-integration mitigated increases in potential nitrification, AOO abundance, and soil nitrate concentrations. The rates of potential nitrification were correlated with the abundance of AOO, highlighting the connection between nitrogen cycling processes and microbial community composition. These patterns in nitrifier abundances, potential nitrification rates, and nitrate levels indicate that the long-term integration of pasture in crop rotations has the potential to reduce early-season nitrogen loss without reducing crop productivity. This work demonstrates how management practices that facilitate favorable interactions between microbial carbon and nitrogen cycling may enhance agroecosystem sustainability and reduce nitrogen pollution.

Effects of macrophytes on potential nitrification and denitrification in oligotrophic lake sediments

Macrophytes may either stimulate or depress nitrogen-related microbial processes via radial oxygen loss (ROL), production of exudates or uptake of inorganic N. ROL can favor aerobic processes as nitrification, exudates may stimulate denitrification, whereas N assimilation and competition with microbes may depress both processes. We measured rates of potential nitrification (PN) and denitrification (PD) in oligotrophic lacustrine sediments colonized by submersed and emergent macrophytes. Potential rates were also analyzed in adjacent control sediments devoid of vegetation. Aim of the work was to verify if the presence of macrophytes alters the potential activity of nitrifying or denitrifying bacteria. Vertical profiles (0−10 cm depth) of PN and PD rates were measured via oxic (nitrification) and anoxic (denitrification) slurries, where we measured the accumulation of NOx− from added NH4+ and the production of 30N2 from added 15NO3−, respectively. Results suggest that under oligotrophic settings macrophytes produced small effects on potential nitrification and denitrification activities. Despite elevated oxygen release demonstrated for most of the tested macrophytes, nitrification was likely constrained by significant plant-bacteria competition. Potential denitrification was comparatively more stimulated by macrophytes, but we address this result to a general increase of heterotrophic microbial activity in organic-richer vegetated sediments, due to dead root biomass or exudates. The highest PN and PD rates were measured in sediments colonized by Littorella uniflora, likely due to its large underground biomass (root:shoot ratio ∼3.5), root porosity and oxygen leakage.

Biomass-Derived Provenance Dominates Glacial Surface Organic Carbon in the Western Himalaya.

The origin, transport pathway, and spatial variability of total organic carbon (OC) in the western Himalayan glaciers are poorly understood compared to those of black carbon (BC) and dust, but it is critically important to evaluate the climatic role of OC in the region. By applying the distribution of OC activation energy; 14C activity; and radiogenic isotopes of 208Pb/204Pb, 207Pb/204Pb, and 206Pb/204Pb in glacial debris and atmospheric particulate matter (PM10 size fraction), we demonstrate that 98.3 ± 1.6 and 1.7 ± 1.6% of OC in western Himalayan glaciers are derived from biomass and petrogenic sources, respectively. The δ13C and N/C composition indicates that the biomass is a complex mixture of C3 vegetation and autochthonous photoautotrophic input modified by heterotrophic microbial activity. The data set reveals that the studied western Himalayan glacier has negligible contributions from fossil-fuel-derived particles, which contrasts to the central and eastern Himalayan glaciers that have significant contributions from fossil fuel sources. We show that this spatial variability of OC sources relates to regional differences in air mass transport pathways and precipitation regimes over the Himalaya. Moreover, our observation suggests that biomass-derived carbon could be the only primary driver of carbon-induced glacier melting in the western Himalaya.

Spatial heterogeneity of organic carbon cycling in sediments of the northern Yap Trench: Implications for organic carbon burial

The hadal trenches (>6000 m) are considered to be ultimate sinks of organic carbon (OC) from biosphere. However, highly spatial heterogeneity of geographic background and organic matter in different zones make significant influences on the OC cycling, and further the carbon burial. In this study, three sediment cores were drilled across the northern Yap Trench axis (9.8–9.9°N, 138.3–138.7°E). The elemental compositions, stable carbon isotopes of organic matter, mineral-specific surface area, and grain size composition were analyzed to investigate the spatial variations of organic sources, distribution, and its degradation in the northern Yap Trench. The surface sedimentary OC (SOC) contents in the northern Yap Trench increase from 0.25% at abyssal depth (4435 m) to 0.50% at hadal depth (~6674 m). Higher OC content (0.27% ± 0.08%) and sedimentation rate (5.8 cm kyr−1) occur in the station on the gradual oceanward slope (~4.2°) compared to those on the steep landward slope (~10°) (0.17% ± 0.13%, 0.52–1.8 cm kyr−1), suggesting enhanced accumulation of OC on the gradual slope. The allochthonous OC (i.e. marine phytoplankton-derived (55% ± 7%) and terrestrial (16% ± 8%)) dominates the SOC pool on the oceanward slope, whereas autochthonous microbe reworked OC contributes more than 50% in the steep landward slope, based on the evaluation of a three-end-member mixing model using δ13C composition and OC/N ratios as source markers. Correspondingly, radiocarbon age of SOC in the gradual slope is ~700 years younger than that in the steep slope with similar depth, indicating that the relatively fresh allochthonous OC is selectively deposited on the gradual slope. A multi-G degradation model demonstrates that OC degradation rates in the northern Yap Trench range from 0.00015 yr−1 to 0.00068 yr−1, which can be comparable with abyssal plain (3000–6000 m) and are lower than those of neritic environments (<1000 m). Mass accumulation model calculation shows that accumulation rate of surface OC in the northern Yap trench is ~2.7 × 10−2 g C m−2 yr−1, much lower than those from other deep ocean seafloors. This study suggests an inefficient SOC preservation within the northern Yap Trench, which might be induced by high labile marine phytoplankton-derived OC inputs and active heterotrophic microbial activity, and the results have important implications for better understanding the effects of sediment dynamics on OC cycling in hadal zones.

Exploration of strategies to increase the nitrogen and phosphate content of solid waste landfill soil.

Several strategies were undertaken to increase the fertility of landfill soil as rapid urbanization remarkably decreases the agricultural land, posing challenges to the fast-growing human population. Towards this direction, soil microcosms were prepared wherein the addition of nutrient or biofertilizer or the combination of both increased the soil nitrogen and phosphate content considerably. The maximum amount of nitrogen fixation and phosphate solubilization occurred in microcosm treated with biofertilizer and nutrient. To investigate the underlying cause, we observed that separate application of nutrient or biofertilizer or combined application of both increased the abundance of nitrogen-fixing and phosphate-solubilizing bacteria in the microcosms. However, the highest abundance of nitrogen-fixing and phosphate-solubilizing bacteria was spotted in a microcosm challenged with nutrient and biofertilizer together. It was detected that with increasing population of nitrogen-fixing and phosphate-solubilizing bacteria, the soil nitrogen and phosphate level also got enhanced, respectively, thus establishing a strong positive correlation between them. The microcosm treated with biofertilizer and nutrient manifested the highest degree of heterotrophic microbial growth and microbial activity than the microcosms either treated with nutrient or biofertilizer. The microcosm treated with nutrient and biofertilizer was found to exhibit the highest functional diversity compared to others. A surface plot was constructed to demonstrate the association among microbial activity, functional diversity, and the availability of soil nitrogen and phosphate content of soil. The result indicates that the combined application of nutrient and biofertilizer increases the microbial activity leading to the formation of a heterogeneous ecosystem that enhances the nitrogen and phosphate content of landfill soil considerably.