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Climate change is the most serious challenge facing humanity. Microbes produce and consume three major greenhouse gases-carbon dioxide, methane, and nitrous oxide-and some microbes cause human, animal, and plant diseases that can be exacerbated by climate change. Hence, microbial research is needed to help ameliorate the warming trajectory and cascading effects resulting from heat, drought, and severe storms. We present a brief summary of what is known about microbial responses to climate change in three major ecosystems: terrestrial, ocean, and urban. We also offer suggestions for new research directions to reduce microbial greenhouse gases and mitigate the pathogenic impacts of microbes. These include performing more controlled studies on the climate impact on microbial processes, system interdependencies, and responses to human interventions, using microbes and their carbon and nitrogen transformations for useful stable products, improving microbial process data for climate models, and taking the One Health approach to study microbes and climate change.

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea.

From 1913 to 1980, two zinc smelters in Palmerton, Pennsylvania, emitted large quantities of atmospheric pollutants nearly eliminating forests along a ridge above the town. In 2008, a remediation treatment was applied to the land above one of the smelters that included the planting of several locally adapted plant species. It also included mineral fertilization and mycorrhizal inoculation. One of the species, the Pitch pine (Pinus rigida, Mill.), is a native tree that is both tolerant of metalliferous soils and obligatorily ectomycorrhizal. This report summarizes the results of two observational studies conducted 5 years after the remediation treatment. The first study's objective was to compare ectomycorrhizal communities on treated Pitch pine saplings, with communities on naturally regenerating saplings in an adjacent non‐remediated area. The second study's objective was to determine if the composition of the fungal communities on root tips of naturally regenerating Pitch pine saplings differed with distance from the smelters. Fungal community compositions were determined using internal transcribed spacer rRNA sequences. Comparisons of sequences from the remediated and non‐remediated sites revealed that communities at the remediated sites had lower taxonomic diversity and were dominated by members of a genus in the remediation inoculant. The results of the smelter‐proximity study indicated that although fungal diversity did not differ markedly with distance from the smelters, the relative abundances of some taxa were greater on saplings growing directly above the smelters, where the soils contained highest concentrations of zinc and cadmium. [ABSTRACT FROM AUTHOR]

The early years of soil genesis during mine spoil reclamation are critical for vegetative establishment and may help predict reclamation success. Mine spoils in the Halle-Leipzig region of Germany were analyzed for microbial changes following a hay mulch-seeding treatment without topsoil or fertilizer application. Microbial biomass carbon ([C.sub.mic]) and dehydrogenase activity (DHA) of spoils were measured each year in the first 3 yr alter treatment. In the third year, bacterial community DNA fingerprints were compared with those from a reference soil. Microbial indicators were measured at three depths in the upper 10 cm of spoils at three sites with contrasting parent materials: glacial till (sandy loam), limnic tertiary sediments (high-lignite sandy clay loam), and quaternary sand and gravel (loamy sand). Before reclamation, [C.sub.mic] means and standard deviations of surface spoils (0-1 cm) were 9 [+ or -] 6, 39 [+ or -] 11, and 38 [+ or -] 16 mg [kg.sup.-1] for the loamy sand, high-lignite sandy clay loam, and sandy loam spoils, respectively. Within one year, mean [C.sub.mic] at the surface increased to 148 [+ or -] 70, 229 [+ or -] 64, and 497 [+ or -] 167 mg [kg.sup.-1], respectively, and was significantly higher at 0 to 1 cm than at lower depths. Highest DHA and DNA yields were obtained in the 0- to 1-cm depth of the sandy loam spoils. Microbial biomass C values exhibited significant correlations with DHA, DNA yield, and extractable C for all three mine spoils. Soil microbial indices were more responsive than plant measurements to differences in parent materials.

Woodlands are pivotal to carbon stocks, but the process of cycling C is slow and may be most effective in the biodiverse root zone. How the root zone impacts plants has been widely examined over the past few decades, but the role of the root zone in decomposition is understudied. Here, we examined how mycorrhizal association and macroinvertebrate activity influences wood decomposition across diverse tree species. Within the root zone of six predominantly arbuscular mycorrhizal (AM) (Acer negundo, Acer saccharum, Prunus serotina, Juglans nigra, Sassafras albidum, and Liriodendron tulipfera) and seven predominantly ectomycorrhizal (EM) tree species (Carya glabra, Quercus alba, Quercus rubra, Betula alleghaniensis, Picea rubens, Pinus virginiana, and Pinus strobus), woody litter was buried for 13 months. Macroinvertebrate access to woody substrate was either prevented or not using 0.22 mm mesh in a common garden site in central Pennsylvania. Decomposition was assessed as proportionate mass loss, as explained by root diameter, phylogenetic signal, mycorrhizal type, canopy tree trait, or macroinvertebrate exclusion. Macroinvertebrate exclusion significantly increased wood decomposition by 5.9%, while mycorrhizal type did not affect wood decomposition, nor did canopy traits (i.e., broad leaves versus pine needles). Interestingly, there was a phylogenetic signal for wood decomposition. Local indicators for phylogenetic associations (LIPA) determined high values of sensitivity value in Pinus and Picea genera, while Carya, Juglans, Betula, and Prunus yielded low values of sensitivity. Phylogenetic signals went undetected for tree root morphology. Despite this, roots greater than 0.35 mm significantly increased woody litter decomposition by 8%. In conclusion, the findings of this study suggest trees with larger root diameters can accelerate C cycling, as can trees associated with certain phylogenetic clades. In addition, root zone macroinvertebrates can potentially limit woody C cycling, while mycorrhizal type does not play a significant role. [ABSTRACT FROM AUTHOR]

Chemical species that are biologically derived, and associated with a particular crop in a farming area, can be more helpful in discriminating soil samples.

A study was conducted to compare the autotrophic ammonia oxidizer population structures in long-term ecological research soils using polymerase chain reaction amplification of microbial community DNA with primers specific for 16S rRNA genes. The comparative study was done to assess the effects of disturbance on certain soil bacteria. Findings revealed that tilled soils contained higher population sizes than native culturable soils.

Research was conducted to examine the influence of soil pH on the compositions of natural populations of autotrophic beta-subroup proteobacterial ammonia oxidizers. A combination of oligonucleotide probing and denaturing gradient gel electrophoresis (DGGE) was used with objective of investigating the hypotheses that Nitrosospira may be significant for ammonia oxidation in acid soils and that the relative abundances of various sequence clusters are related to soil pH. Results reveal the value of DGGE and suggests that Nitrosospira cluster 2 may be important for ammonia-oxidizing activity in acid soils.

The sodium dodecyl sulfate (SDS) method of bacterial DNA extraction from soils is simple, quick and efficient. The method involves bacterial lysis with a high-salt extraction buffer, followed by the heating of the soil suspension with SDS, hexadecyltrimethylammonium bromide and proteinase K. A combination of SDS with grinding and freezing-thawing increases the DNA extraction efficiency. The best DNA purification method is the gel-plus-minicolumn method. The gel-plus-concentration method gives the highest DNA recovery rate.

With a multitude of physical, biological, and chemical soil characteristics disrupted or degraded during surface mining, it is challenging to achieve proper reclamation, much less restoration, post‐mining. We sought to assess the potential of a native wildflower seed mix (NWSM) to establish and achieve high vegetative coverage in the first season using soil amendments. We also evaluated the influence of amendments on community composition and soil quality. In May 2018, we seeded a NWSM on a surface mine in experimental plots treated with either inorganic fertilizer, spent mushroom compost, or left untreated. Plant coverage and community composition within experimental plots were assessed in October 2018. Soil samples were collected at the beginning and end of the season to identify potential changes in organic carbon, nitrogen availability, bulk density, and pH. First‐season vegetation results indicate that soil amendments may not be ecologically necessary or economically sensible for initial revegetation using a NWSM. Unamended plots surpassed compost‐amended plots and equaled or surpassed fertilizer‐amended plots in coverage, species richness, and proportion of seedlings present that originated from the mix. However, results from soil analyses suggest that compost may be beneficial to meeting surface mine restoration goals by improving important soil characteristics, such as percent organic matter, labile carbon, nitrate content, and pH, that could aid ecosystem recovery. Given the high degree of heterogeneity both within and between surface mines, future work should focus on identifying initial soil characteristics that could enable land managers to meet both reclamation and restoration goals using a NWSM. [ABSTRACT FROM AUTHOR]

The results from performance analysis of a single-chamber microbial fuel cell (MFC) to remove chemical odors from swine wastewater are presented. The results indicated that MFCs made it possible not only to accelerate the rate of odor removal, but was also found to be effective in removing organic matter and producing electricity.

A novel approach to swine waste odor reduction is investigated in the form of the addition of FeCl3, a commonly used coagulant in municipal wastewater treatment, to stimulate degradation of odorous compounds by dissimilatory iron-reducing bacteria (DIRB). DNA sequences obtained from rRNA gene amplicons of bacterial communities in FeCl3-treated microcosms were closely related to Desulfitobacterium spp., which are known representatives of DIRB.

Excessive N and P in surface waters can promote eutrophication (algae‐dominated, low‐O2 waters), which decreases water quality and aquatic life. Duckweed (Lemnaceae), a floating aquatic plant, rapidly absorbs N and P from water and its composition shows strong potential as a soil amendment. Therefore, it may be used to transfer N and P from eutrophic water bodies to agricultural fields. In this work, dried duckweed was incorporated into agricultural soil in microcosm, column, and field tests to evaluate biological N cycling, nutrient retention, and crop yield compared with compost, diammonium phosphate (DAP), and an amendment‐free control. In microcosm tests, 25 ± 13% of duckweed N was mineralized, providing on average less mineral N than DAP (107 ± 21%), but more than compost (11 ± 12%). In columns, duckweed treatments leached only 2% of the N added, significantly less than DAP, which leached 60% of its N. Compared with the control, DAP leached significantly more phosphate (78%), whereas duckweed and compost treatments leached less (56 and 27%, respectively). Crop yield, as well as runoff N and P, were measured in field tests growing forage sorghum [Sorghum bicolor (L.) Moench.]. Although less total N was applied to duckweed plots than to DAP plots (75 vs. 130 kg ha−1, respectively), duckweed was found to retain 30% more total mineral N in a tilled agricultural field than DAP, while supporting a comparable yield. These tests indicate that duckweed may provide a sustainable source of N and P for agriculture. Core Ideas: In microcosm tests, 25% of organic N in duckweed was mineralized within 5 d.In 22‐d column tests, duckweed leached only 2% of the N applied from its biomass.In 22‐d column tests, duckweed leached 56% less phosphate than the control.In field tests, duckweed reduced inorganic N runoff by 30% compared with mineral fertilizer.In field tests, sorghum yield was comparable for duckweed and mineral fertilizer treatments. [ABSTRACT FROM AUTHOR]

At a 50-year-old coal mine drainage barrens in central Pennsylvania, USA, we evaluated the biogeochemistry of acidic, Fe(III)oxy(hydr)oxide precipitates in reclaimed plots and compared them to untreated precipitates in control areas. Reclaimed plots supported successional vegetation that became established after a one-time compost and lime treatment in 2006, while control plots supported biological crusts. Precipitates were sampled from moist yet unsaturated surface layers in an area with lateral subsurface flow of mine drainage above a fragipan. Fe(II) concentrations were three- to five-fold higher in reclaimed than control precipitates. Organically bound Fe and amorphous iron oxides, as fractions of total Fe, were also higher in reclaimed than control precipitates. Estimates of Fe-reducing and Fe-oxidizing bacteria were four- to tenfold higher in root-adherent than both types of control precipitates. By scaling up measurements from experimental plots, total Fe losses during the 5-yr following reclamation were estimated at 45 t Fe ha−1 yr−1. [Copyright &y& Elsevier]

Acid mine drainage ( AMD) barrens result from destruction of vegetation within AMD flow paths. When exposed to air, soluble iron in AMD undergoes oxidation and hydrolysis to form ferric iron (oxyhydr)oxides which accumulate on soil surfaces. A restoration experiment was conducted at a 50-year-old AMD barrens created by discharge from an abandoned underground coal mine. The objective was to determine whether vegetation could be established by altering rather than removing surface layers of acidic precipitates at a site representative of other mining-degraded areas. Three zones in the barrens were identified based on moisture content, pH (2.7-3.3), and thickness of precipitates (0-35 cm). Our hypothesis was that application of the same reclamation method to all zones would fail to sustain >70% vegetative cover in each zone after four growing seasons. The method consisted of applying 11 t/ha lime and 27 or 54 t/ha compost before rototilling (top 15 cm) and mulching with oat straw containing viable seeds for a nurse crop. Lime-only plots were included for comparison, and all amended plots were sown with a mine reclamation seed mix. Oats, sown species, and indigenous species dominated cover in the first, second, and fourth growing seasons, respectively. In the fourth year following reclamation, compost-amended plots had >70% cover and improved soil properties in all three zones, providing evidence to reject our hypothesis. Vegetative restoration of AMD barrens did not require removal of highly acidic precipitates, since they could be transformed at low-cost into a medium that supports indigenous plants. [ABSTRACT FROM AUTHOR]

Abstract: Soil microbial habitats are altered by mulching, a common practice in urban areas during which vegetation is removed and soils covered to suppress weeds and retain moisture. Soil microorganisms drive nitrogen-cycling processes in mulched soils, because living plants no longer take up ammonium-N released during decomposition of residual organic matter. Because ammonia oxidizers carry out the first, rate-limiting step of nitrification, we compared ammonia oxidizers in experimental, unfertilized plots of mulched and vegetated soils. We hypothesized that mulched and vegetated soils would support contrasting communities of bacterial and archaeal ammonia oxidizers, as determined by quantitative PCR and primers specific for genes encoding ammonia monooxygenase subunit A (amoA). Clone libraries of archaeal amoA also were constructed to compare diversity in soil cores, duplicate blocked plots, and treatments (bark-mulched, gravel-mulched, and unmanaged old field vegetation). Gene copies from ammonia-oxidizing bacteria (AOB) ranged from 2.2 × 106 to 2.7 × 107 gene copies per gram dry soil and did not differ across treatments. In contrast, gene copies from ammonia-oxidizing archaea (AOA) ranged from 9.1 × 105 to 1.0 × 108 copies per gram dry soil, with bark-mulched soils having significantly lower abundance. Community structure of AOA in gravel-mulched soils was distinct from the other two treatments. At 97% amino acid similarity, 22 operational taxonomic units, or OTUs, were identified, with only one OTU found in all 18 clone libraries. This ubiquitous OTU-1, which was highly similar to published amoA sequences recovered from soils, comprised 55% of all 482 translated sequences. Greater variability in OTU richness was observed among cores from mulched soils than from vegetated soils. Our observations supported our hypothesis that AOA communities differ in mulched and vegetated soils, with mulched soils providing altered and variable microniches for these N cycling microorganisms. [Copyright &y& Elsevier]

Quartz diorite bedrock underlying the Luquillo Mountains of eastern Puerto Rico undergoes weathering at one of the fastest documented rates for granitic rocks in the world. Although tropical temperatures and precipitation promote rapid weathering in this location, increased bacterial densities in the regolith immediately above the bedrock suggest that microorganisms contribute to mineral weathering as well. Deep saprolite and saprock samples were obtained at the bedrock interface in an upland location (Guaba Ridge) in the Rio Icacos watershed for examination by environmental scanning electron microscopy (ESEM). In ESEM images, mineral nanotubes were observed to occur frequently in association with coccus- and rod-shaped structures resembling bacteria. These nanotubes (50-140-nm width and 150-2700-nm length) were identified as halloysite using transmission electron microscopy. Observations of multiple nanotubes on the surfaces of an individual cell are consistent with the cell's exterior functional groups interacting with Si in pore water to facilitate halloysite nucleation. We propose that one mechanism by which bacteria contribute to the rapid weathering of quartz diorite minerals in this regolith is by lowering the free energy for secondary mineral formation. The presence of bacterial surfaces may result in more rapid removal of Si from solution, thereby increasing the dissolution rates of primary minerals. [ABSTRACT FROM AUTHOR]

We characterized the microbiologically mediated oxidative precipitation of Fe(II) from coalmine-derived acidic mine drainage (AMD) along flow-paths at two sites in northern Pennsylvania. At the Gum Boot site, dissolved Fe(II) was efficiently removed from AMD whereas minimal Fe(II) removal occurred at the Fridays-2 site. Neither site received human intervention to treat the AMD. Culturable Fe(II) oxidizing bacteria were most abundant at sampling locations along the AMD flow path corresponding to greatest Fe(II) removal and where overlying water contained abundant dissolved O2. Rates of Fe(II) oxidation determined in laboratory-based sediment incubations were also greatest at these sampling locations. Ribosomal RNA intergenic spacer analysis and sequencing of partial 16S rRNA genes recovered from sediment bacterial communities revealed similarities among populations at points receiving regular inputs of Fe(II)-rich AMD and provided evidence for the presence of bacterial lineages capable of Fe(II) oxidation. A notable difference between bacterial communities at the two sites was the abundance of Chloroflexi-affiliated 16S rRNA gene sequences in clone libraries derived from the Gum Boot sediments. Our results suggest that inexpensive and reliable AMD treatment strategies can be implemented by mimicking the conditions present at the Gum Boot field site.The ISME Journal (2008) 2, 1134–1145; doi:10.1038/ismej.2008.60; published online 12 June 2008 [ABSTRACT FROM AUTHOR]

This article investigates the physicochemical characteristics of animal and municipal wastes decomposed in arid soils. It is worth noting that the application of anaerobically processed animal manure to maintain adequate levels of organic matter in arid soils is becoming a common practice. The purpose of this study was to characterize two farm manure products as compared with municipal waste compost. Farmyard manure and biogas manure products were obtained by processing fresh dairy feces. The farmyard manure was composted in windows under aerobic conditions, and the biogas manure was processed anaerobically in a biogas generator. The comparisons were based on determining the chemical composition and biochemical characteristics of the three organic materials and monitoring biodegradation rates of these products in two arid soils under controlled aerobic conditions. The anaerobic processing to obtain a biogas manure product was much faster than the aerobic composting of farmyard manure.

Hydrogen gas (~60% H2) was produced in a continuous flow bioreactor inoculated with heat-treated soil, and fed synthetic wastewater containing glucose (9.5 g l-1). The pH in the bioreactor was maintained at 5.5 to inhibit consumption of H2 by methanogens. The objective of this study was to characterize bacterial communities in the reactor operated under two different hydraulic retention times (HRTs of 30-h and 10-h) and temperatures (30°C and 37°C). At 30-h HRT, the H2 production rate was 80 ml h-1 and yield was 0.91 mol H2/mol glucose. At 10-h HRT, the H2 production rate was more than 5 times higher at 436 ml h-1, and yield was 1.61 mol H2/mol glucose. Samples were removed from the reactor under steady-state conditions for PCR-based detection of bacterial populations by ribosomal intergenic spacer analysis (RISA). Populations detected at 30-h HRT were more diverse than at 10-h HRT and included representatives of Bacillaceae, Clostridiaceae, and Enterobacteriaceae. At 10-h HRT, only Clostridiaceae were detected. When the temperature of the 10-h HRT reactor was increased from 30°C to 37°C, the steady-state H2 production rate increased slightly to 463 ml h-1 and yield was 1.8 mol H2/mol glucose. Compared to 30°C, RISA fingerprints at 37°C from the 10-h HRT bioreactor exhibited a clear shift from populations related toClostridium acidisoli(subcluster Ic) to populations related toClostridium acetobutylicum(subcluster Ib). [ABSTRACT FROM AUTHOR]

Soil is a complex habitat for diverse biota. A significant challenge in teaching soil ecology is our inability to observe organisms as they live and interact in the soil. The objective of this article is to describe an interactive class project to help students visualize the sizes of different groups of soil organisms and to relate these to soil structural components. This project was carried out by students in an upper-level undergraduate soil ecology class. It involved the design and construction of a 4000x scale model of a soil aggregate and its associated organisms. The body of the model was made from inexpensive, lightweight materials and had a diameter of approximately 1 m to depict a 0.25-mm aggregate. Students identified and discussed appropriate size ranges and construction materials for the model's bacteria, fungi, nematodes, mites, springtails, and other components. Instructor-guided questions addressed size and arrangement of sand, silt, and clay particles; pores; and organic matter in a typical soil aggregate. The model is a useful tool for conveying physical and ecological relationships among soil organisms and is adaptable for use at diverse educational levels. [ABSTRACT FROM AUTHOR]

Low-pH and low-nutrient conditions make the establishment of vegetation in mining-impacted environments particularly challenging. This study was conducted on soils forming from secondary Fe mineral precipitates in experimental plots at a 50-year-old acid mine drainage (AMD) barrens in Central Pennsylvania, U.S.A. Our objective was a qualitative assessment of bacterial and eukaryal diversity in reclaimed precipitates supporting dense successional vegetation six years after a single addition of lime (to raise pH from 2.5 to 4.5) and a single incorporation of compost. At the time of sampling, the pH of reclaimed precipitates had declined to initial values (2.5–2.7) and was similar to that of control precipitates supporting indigenous biological crusts. Microbial diversity was compared using 454 pyrosequencing of 16S rRNA genes (V1-V5) and 18S rRNA (V4-V5) in upper layers (adhering to roots and crusts) and lower layers (below roots and crusts). A total of 1721 bacterial OTUs at 97% similarity and 307 eukaryal OTUs at 97% similarity were recognized in the entire dataset. Despite similar pH, reclaimed precipitates had more diversity than control precipitates. Proteobacteria and Actinobacteria were the most abundant bacterial phyla in reclaimed and control precipitates, respectively. Acidobacteri a were more abundant in root-and crust-enriched layers than in the underlying precipitates containing less carbon. Basidiomycota fungi were the most abundant classified eukaryotes in reclaimed precipitates, while Bryophyta dominated control precipitates. Glomeromycota were observed in reclaimed but not in control precipitates, where Ascomycota were the most abundant fungi. After the one–time reclamation approach, bacterial richness in AMD precipitates was three-fold lower than that determined for acid sulfate soils using closed reference OTU picking. These results suggested the need for further lime and compost incorporation to increase soil functionality. [ABSTRACT FROM AUTHOR]

Headwater riparian wetlands are relatively small in size but functionally significant as expected hot spots of microbial activity in the landscape. Despite their roles as biogeochemical drivers, little is known about how microbial communities in headwater riparian wetlands are affected by surrounding land-uses and land-covers (LULCs). The primary objective of this study was to determine if and how wetland soil microbial abundance and community composition varied as a function of landscape metrics as mediated through on-site edaphic properties. Forty-two soil samples, collected from eight headwater riparian wetlands in the Ridge and Valley Region of central Pennsylvania, were used for phospholipid fatty acid (PLFA) profiling of soil microbial communities. These samples were used to create microbial habitat models describing plot-level relationships between edaphic properties and microbial measures (i.e., microbial biomarker abundances, ratios and composition). Soil organic matter (SOM) content was a strong predictor of microbial biomarker abundances and fungi/bacteria ratios, while soil pH was a strong predictor of microbial composition (i.e., relative abundance of individual fatty acids) and potential microbial stress indices (i.e., cy19:0a/18:1ω7c and cy17:0/16:1ω7c ratios). Soil texture, soil moisture, and litter total nitrogen had smaller, but significant effects in these empirical microbial habitat models. Microbial habitat models were subsequently used to estimate microbial measures for a larger regional headwater riparian wetland dataset (n = 87), where edaphic property information was compiled. Site-average microbial measures were correlated with wetland elevation, and with landscape composition metrics in a landscape assessment area (i.e., 125,664 m 2 ). Wetland elevation explained high among-site variability in microbial abundance measures, as mediated through SOM content, in headwater riparian wetlands in forested landscapes. However, wetland elevation was confounded by landscape composition, for headwater riparian wetland in mixed forested-agricultural landscapes. Hydrology, geomorphology, and changes in vegetation could be used to explain SOM variation across wetland elevation and variability in surrounding landscape composition. Microbial composition measures, including the cy19:0/18:1ω7c ratio and principal component (PC) axes derived from 23 individual PLFA biomarkers were negatively related to the Landscape Development Intensity (LDI) index, and the percent area of row crops, pastures and grasslands, and positively related to the percent area of forest. The cy17:0/16:1ω7c ratio was positively related to the LDI index, and the percent area of pasture and grasslands, and negatively related to the percent area of forest and wetland elevation. Differences along PC axes were most clearly related to the relative abundances of fungal communities; headwater riparian wetland in forested landscapes had significantly higher relative abundances of saprophytic fungi biomarkers, while headwater riparian wetland in mixed landscapes had significantly higher relative abundances of the arbuscular mycorrhizal fungi biomarker. This study highlights the utility of simple landscape metrics, which describe wetland position and landscape composition, for predicting differences in edaphic variability and associated microbial community composition and biomass among headwater riparian wetlands at a regional scale. [ABSTRACT FROM AUTHOR]

Abstract: Peatlands effectively retain heavy metals and prevent stream and watershed contamination. Sulfate reduction is considered the most significant process of metal immobilization in natural wetlands and microbial sulfate reduction is the presumed mechanism that results in the precipitation of metal sulfides. In this study, we examined the biogeochemical mechanisms involved in zinc retention and accumulation in a metalliferous peatland of western New York. In the reducing conditions of these peatlands zinc sulfides occurred as framboidal aggregates of sphalerite and polytypic wurtzite (2nH, n ⩾2) nanocrystallites associated with bacterial cells and organic matter. Bacterial cells were co-located with ZnS inside peat particles where the microenvironment remained anoxic. The peat zinc sulfide was depleted in 34S isotopes relative to the sulfate supplied to the peatland by 18–34 per mill, implicating its biological formation. Extraction of microbial community DNA from peat samples yielded diverse PCR amplicons from dissimilatory sulfite reductase (dsrAB) genes, indicating varied bacterial taxa capable of reducing forms of oxidized sulfur. Nanocrystals with distinct structural features were observed in samples containing contrasting dsrAB sequences. The results of this investigation provide clear evidence that microorganisms can influence the chemical forms of heavy metals in peatland environments. Our findings also provide insight into the conditions necessary to promote the immobilization of chalcophile elements in engineered systems for the treatment of acid mine drainage and wastewater effluents. [Copyright &y& Elsevier]

Abstract: Enzymes that have proven to be capable of removing toxic compounds from water and soil may also be useful in the deodorization of animal manures. Considering that pork production in the US is a $40-billion industry with over half a million workers, odor control to protect air quality in the neighboring communities must be considered an essential part of managing livestock facilities. This pilot scale (20–120L) study tested the use of minced horseradish (Armoracia rusticana L.) roots (1:10 roots to swine slurry ratio), with calcium peroxide (CaO2 at 34mM) or hydrogen peroxide (H2O2 at 68mM), to deodorize swine slurry taken from a 40,000-gallon storage pit at the Pennsylvania State University’s Swine Center. Horseradish is known to contain large amounts of peroxidase, an enzyme that, in the presence of peroxides, can polymerize phenolic odorants and thus reduce the malodor. Twelve compounds commonly associated with malodor (seven volatile fatty acids or VFAs, three phenolic compounds and two indolic compounds) were used as odor indicators. Their concentration in swine slurry before and after treatment was determined by gas chromatography (GC) to assess the deodorization effect. The pilot scale testing demonstrated a complete removal of phenolic odorants (with a detection limit of 0.5mgL−1) from the swine slurry, which was consistent with our previous laboratory experiments using 30-mL swine slurry samples. Horseradish could be recycled (reused) five times while retaining significant reduction in the concentration of phenolic odorants. In view of these findings, inexpensive plant materials, such as horseradish, represent a promising tool for eliminating phenolic odorants from swine slurry. [Copyright &y& Elsevier]

Between 62% and 92% of industrial and municipal wastewater in upper-middle, low-middle, and low income countries is discharged to the environment untreated, releasing valuable nutrients such as nitrogen (N) and phosphorus (P) into rivers, lakes, and oceans (Lipponen and Nikiforova, 2017). This, in addition to excess nutrients often present in agricultural runoff due to overuse and misuse of fertilizers, can lead to eutrophication, often causing irreparable damage to aquatic ecosystems. For these reasons, new techniques must be found to effectively recover waste nutrients and upcycle them into natural soil amendments that can be used to enrich soil quality and grow food for future generations while minimizing agricultural runoff. Duckweed is a small floating aquatic plant that can hyperaccumulate nutrients present in wastewater and agricultural runoff and then be harvested and reused to replace or supplement commercial soil fertilizers. As part of a two-year field trial, duckweed was tested for the second consecutive year in this study as a soil amendment in comparison to, and in combination with, commercial fertilizer for the growth of sorghum, a drought-resistant grain. Relative to fertilizer in all cases, soils amended with duckweed generated less ammonia and nitrate in surficial runoff. No differences in P in cumulative runoff were found among the different treatments (p = 0.509). Additionally, duckweed application produced sorghum grains with greater N and P content than other treatments (1.63 ± 0.03% N (p = 0.001) and 0.35 ± 0.0% P (p = 0.016)). Duckweed treatments also showed increased soil residue carbon and P after harvesting the crop. When normalized by germination rate, sorghum yield was similar across treatments. In agreement with first-year findings, the results indicated that duckweed may be a viable alternative to commercial fertilizer from an environmental and agricultural perspective, providing acceptable yields and contributing to the buildup of beneficial nutrients in the soil profile. Additional testing is needed to further evaluate potential germination inhibitors, greenhouse gas emissions (ex., N 2 O), and efficacy when applied to different crops and soil types. • Nutrients in wastewater can be recovered by duckweed and reused in agriculture. • Duckweed amendments enrich soils by contributing beneficial nutrients. • Duckweed provides a slow release of nutrients over time for crop growth. • Soils amended with duckweed generate less ammonia and nitrate in surficial runoff. • Duckweed produces sorghum grains with greater N and P content than other treatments. [ABSTRACT FROM AUTHOR]

Manipulating the taxonomic richness of communities can impact numerous community functions. One proposed explanation is that certain taxa can exploit resources or habitat space that others cannot, leading to additive contributions to process rates. It is of interest to learn whether the reverse could also be true. That is, can increasing the richness of resources in an environment impact community size, composition, and function? We mimicked hydrocarbon spills in an uncontaminated soil by introducing individual substrates and all possible combinations of hexadecane, fluorene, and pyrene at four total concentrations, along with a crude oil treatment. We hypothesized that increasing substrate richness would increase microbial abundance, diversity, and function. When a single hydrocarbon substrate was added, we observed lower bacterial and fungal abundance (qPCR) relative to controls receiving no hydrocarbons. Interestingly, however, regardless of total hydrocarbon concentration, microbial abundance increased as the number of added substrates increased. We observed large changes in microbial composition, diversity, and hydrocarbon loss based on specific hydrocarbon substrate combinations, but this was not clearly linked to hydrocarbon substrate richness. These results show that introduced hydrocarbon richness has a strong influence on microbial abundance, but that changes to other soil processes may depend more on other properties of the added compounds. [ABSTRACT FROM AUTHOR]

Worldwide, arable soils have been degraded through erosion and exhaustive cultivation, and substantial proportions of fertilizer nutrients are not taken up by crops. A central challenge in agriculture is to understand how soils and resident microbial communities can be managed to deliver nutrients to crops more efficiently with minimal losses to the environment. Throughout much of the twentieth century, intensive farming has caused substantial loss of organic matter and soil biological function. Today, more farmers recognize the importance of protecting soils and restoring organic matter through reduced tillage, diversified crop rotation, cover cropping, and increased organic amendments. Such management practices are expected to foster soil conditions more similar to those of undisturbed, native plant-soil systems by restoring soil biophysical integrity and re-establishing plant-microbe interactions that retain and recycle nutrients. Soil conditions which could contribute to desirable shifts in microbial metabolic processes include lower redox potentials, more diverse biogeochemical gradients, higher concentrations of labile carbon, and enrichment of carbon dioxide (CO 2 ) and hydrogen gas (H 2 ) in soil pores. This paper reviews recent literature on generalized and specific microbial processes that could become more operational once soils are no longer subjected to intensive tillage and organic matter depletion. These processes include heterotrophic assimilation of CO 2 ; utilization of H 2 as electron donor or reactant; and more diversified nitrogen uptake and dissimilation pathways. Despite knowledge of these processes occurring in laboratory studies, they have received little attention for their potential to affect nutrient and energy flows in soils. This paper explores how soil microbial processes could contribute to in situ nutrient retention, recycling, and crop uptake in agricultural soils managed for improved biological function., Competing Interests: Conflict of Interest: All authors declare no conflict of interest in this paper.

Traditionally, studies in microbial genomics have focused on single-genomes from cultured species, thereby limiting their focus to the small percentage of species that can be cultured outside their natural environment. Fortunately, recent advances in high-throughput sequencing and computational analyses have ushered in the new field of metagenomics, which aims to decode the genomes of microbes from natural communities without the need for cultivation. Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic sequence data. Current tools and techniques are reviewed in this paper which address challenges in 1) genomic fragment annotation, 2) phylogenetic reconstruction, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology.

A single-chamber microbial fuel cell (MFC) was used to reduce 10 chemicals associated with odors by 99.76% (from 422 +/- 23 mug/ml) and three volatile organic acids (acetate, butyrate, and propionate) by >99%. The MFC produced a maximum of 228 mW/m(2) and removed 84% of the organic matter in 260 h. MFCs were therefore effective at both treatment and electricity generation.

Public concerns about offensive odors from livestock manures are on the rise and so is the pressure to develop practical ways to reduce the odors. The use of minced horseradish (Armoracia rusticanaL) roots (1:10 w/v plant tissue to swine slurry ratio), with calcium peroxide (CaO2 at 26 or 34 mM) or hydrogen peroxide (H2O2 at 34, 52, or 68 mM) for the deodorization of swine manure, was evaluated through a series of laboratory experiments. The principle underlying this deodorization method is the oxidation of odorants by the concerted action of horseradish peroxidase (present in the plant tissue) and peroxide that serves as an electron acceptor, followed by polymerization of phenolic odorants with a possible copolymerization or adsorption of other odorant compounds. The deodorization effect was assessed by a human panel and gas chromatography (GC). In the case of the GC method, 12 compounds commonly associated with malodor (7 volatile fatty acids or VFAs, 3 phenolic compounds, and 2 indolic compounds) were used as odor indicators. Malodor assessment of the treated slurry by a human panel indicated a 50% reduction in odor intensity. GC results showed 100% removal of all phenolic odorants without reoccurrence for at least 72 h. In view of these data, using plant materials as enzyme carriers and peroxides as electron acceptors emerges as an effective approach to phenolic odor control in animal manure.