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At least 109 records · Page 6Linked to original sources

What could explain δ13C signatures in biocrust cyanobacteria of drylands?

Dryland ecosystems are increasing in geographic extent and contribute greatly to interannual variability in global carbon dynamics. Disentangling interactions among dominant primary producers, including plants and autotrophic microbes, can help partition their contributions to dryland C dynamics. We measured the δ 13 C signatures of biological soil crust cyanobacteria and dominant plant species (C 3 and C 4 ) across a regional scale in the southwestern USA to determine if biocrust cyanobacteria were coupled to plant productivity (using plant-derived C mixotrophically), or independent of plant activity (and therefore purely autotrophic). Cyanobacterial assemblages located next to all C 3 plants and one C 4 species had consistently more negative δ 13 C (by 2‰) than the cyanobacteria collected from plant interspaces or adjacent to two C 4 Bouteloua grass species. The differences among cyanobacterial assemblages in δ 13 C could not be explained by cyanobacterial community composition, photosynthetic capacity, or any measured leaf or root characteristics (all slopes not different from zero). Thus, microsite differences in abiotic conditions near plants, rather than biotic interactions, remain a likely mechanism underlying the observed δ 13 C patterns to be tested experimentally.

New Mexico

Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities

Over the past decade, an abundance of 16S rRNA gene surveys have provided microbiologists with data regarding the prokaryotes present in a coral-associated microbial community. Functional gene studies that provide information regarding what those microbes might do are fewer, particularly for non-tropical corals. Using the GeoChip 5.0S microarray, we present a functional gene study of microbiomes from five species of cold-water corals collected from depths of 296–1567 m. These species included two octocorals, Acanthogorgia aspera and Acanthogorgia spissa , and three stony corals: Desmophyllum dianthus , Desmophyllum pertusum (formerly Lophelia pertusa ), and Enallopsammia profunda . A total of 24,281 gene sequences (representing different microbial taxa) encoding for 383 functional gene families and representing 9 metabolic gene categories were identified. Gene categories included metabolism of carbon, nitrogen, phosphorus, and sulfur, as well as virulence, organic remediation, metal homeostasis, secondary metabolism and phylogeny. We found that microbiomes from Acanthogorgia spp. were the most functionally distinct but also least diverse compared against those from stony corals. Desmophyllum spp. microbiomes were more similar to each other than to E. profunda . Of 383 total gene families detected in this study, less than 20% were significantly different among these deep-water coral species. Similarly, out of 59 metabolic sub-categories for which we were able to make a direct comparison to microbiomes of tropical corals, only 7 were notably different: anaerobic ammonium oxidation (anammox), chitin degradation, and dimethylsulfoniopropionate (DMSP) degradation, all of which had higher representations in deep-water corals; and chromium homeostasis/resistance, copper homeostasis/resistance, antibiotic resistance, and methanogenesis, all of which had higher representation in tropical corals. This implies a broad-scale convergence of the microbial functional genes present within the coral holobiont, independent of coral species, depth, symbiont status, and morphology.

Coral Reefs

Assessment of antibiotic resistance genes in Caribbean corals, including those treated with amoxicillin

The decimation of reefs from stony coral tissue loss disease prompted the use of a topical amoxicillin treatment to prevent coral mortality. Application of this treatment led to concerns about unintentional impacts such as potential alteration of the coral microbiome and possible spread of antibiotic resistance. We used three different methodologies—microbial RNA sequencing, 16S rRNA amplicon surveys, and microbial qPCR array—to assess these concerns and to establish a baseline of antibiotic resistance genes (ARGs) in untreated coral microbes. We conducted microbial RNA sequencing on wild Montastraea cavernosa coral mucus samples collected before and 24 h after amoxicillin application. While diverse antibiotic resistance genes (ARGs) were expressed, no differences in ARG expression were detected after amoxicillin treatment. Additionally, there were no notable changes in the microbial communities between the before and after samples. In a separate experiment, a microbial qPCR array was used to assess differences in ARGs over longer timescales using cores from wild Colpophyllia natans , comparing never-treated corals with ones treated a single time seven months prior and with those treated multiple times seven months and more prior. No clinically relevant ARGs were detected across any samples. A small number of above-detection reads (4 in the never-treated corals, 2 in the once-treated corals, and 0 in the multi-treated corals) may indicate weak amplification of similar environmental (non-anthropogenic) ARGs in the corals. Results indicate that the localized topical application of amoxicillin to prevent mortality of SCTLD-affected corals does not: (1) significantly disrupt microbiomes, (2) increase ARG expression in adjacent tissues of these species within 24 h, nor (3) increase abundance of clinically relevant ARGs over a 7 month time period.

Florida

Symbiotic nitrogen fixation does not stimulate soil phosphatase activity under temperate and tropical trees

Symbiotic nitrogen (N)-fixing plants can enrich ecosystems with N, which can alter the cycling and demand for other nutrients. Researchers have hypothesized that fixed N could be used by plants and soil microbes to produce extracellular phosphatase enzymes, which release P from organic matter. Consistent with this speculation, the presence of N-fixing plants is often associated with high phosphatase activity, either in the soil or on root surfaces, although other studies have not found this association, and the connection between phosphatase and rates of N fixation—the mechanistic part of the argument—is tenuous. Here, we measured soil phosphatase activity under N-fixing trees and non-fixing trees transplanted and grown in tropical and temperate sites in the USA: two sites in Hawaii, and one each in New York and Oregon. This provides a rare example of phosphatase activity measured in a multi-site field experiment with rigorously quantified rates of N fixation. We found no difference in soil phosphatase activity under N-fixing vs. non-fixing trees nor across rates of N fixation, though we note that no sites were P limited and only one was N limited. Our results add to the literature showing no connection between N fixation rates and phosphatase activity.

Oecologia

Quantification of the nitrogen cycle in a prairie stream

Nitrogen (N) was added for 35 days in the form of 15 NH 4 Cl to Kings Creek on Konza Prairie, Kansas. Standing stocks of N in key compartments (that is, nutrients, detritus, organisms) were quantified, and the amount of labeled N entering the compartments was analyzed. These data were used to calculate turnover and flux rates of N cycling through the food web, as well as nutrient transformation rates. Inorganic N pools turned over much more rapidly in the water column of this stream than in pelagic systems where comparable measurements have been made. As with other systems, the mass of ammonium was low but it was the key compartment mediating nutrient flux through the ecosystem, whereas dissolved organic N, the primary component of N flux through the system, is not actively cycled. Nitrification was also a significant flux of N in the stream, with rates in the water column and surface of benthos accounting for approximately 10% of the total ammonium uptake. Primary consumers assimilated 67% of the inorganic N that entered benthic algae and microbes. Predators acquired 23% of the N that consumers obtained. Invertebrate collectors, omnivorous crayfish ( Orconectes spp.), and invertebrate shredders dominated the N flux associated with primary consumers. Mass balance calculations indicated that at least 23% of the 309 mg of 15 N added during the 35 days of release was retained within the 210-m stream reach during the release. Overall, the rates of turnover of N in organisms and organic substrata were significantly greater when C:N was low. This ratio may be a surrogate for biological activity with regard to N flux in streams.

Kansas

To understand coral disease, look at coral cells

Diseases threaten corals globally, but 40 years on their causes remain mostly unknown. We hypothesize that inconsistent application of a complete diagnostic approach to coral disease has contributed to this slow progress. We quantified methods used to investigate coral disease in 492 papers published between 1965 and 2013. Field surveys were used in 65% of the papers, followed by biodetection (43%), laboratory trials (20%), microscopic pathology (21%), and field trials (9%). Of the microscopic pathology efforts, 57% involved standard histopathology at the light microscopic level (12% of the total investigations), with the remainder dedicated to electron or fluorescence microscopy. Most (74%) biodetection efforts focused on culture or molecular characterization of bacteria or fungi from corals. Molecular and immunological tools have been used to incriminate infectious agents (mainly bacteria) as the cause of coral diseases without relating the agent to specific changes in cell and tissue pathology. Of 19 papers that declared an infectious agent as a cause of disease in corals, only one (5%) used microscopic pathology, and none fulfilled all of the criteria required to satisfy Koch’s postulates as applied to animal diseases currently. Vertebrate diseases of skin and mucosal surfaces present challenges similar to corals when trying to identify a pathogen from a vast array of environmental microbes, and diagnostic approaches regularly used in these cases might provide a model for investigating coral diseases. We hope this review will encourage specialists of disease in domestic animals, wildlife, fish, shellfish, and humans to contribute to the emerging field of coral disease.

EcoHealth

Non-spore forming eubacteria isolated at an altitude of 20,000 m in Earth's atmosphere: extended incubation periods needed for culture-based assays

On 13 August 2004, an atmospheric sample was collected at an altitude of 20,000 m along a west to east transect over the continental United States by NASA’s Stratospheric and Cosmic Dust Program. This sample was then shipped to the US Geological Survey’s Global Desert Dust program for microbiological analyses. This sample, which was plated on a low nutrient agar to determine if cultivable microorganisms were present, produced 590 small yellow to off-white colonies after approximately 7 weeks of incubation at room-temperature. Of 50 colonies selected for identification using 16S rRNA sequencing, 41 belonged to the family Micrococcaceae , seven to the family Microbacteriaceae , one to the genus Staphylococcus , and one to the genus Brevibacterium . All of the isolates identified were non-spore-forming pigmented bacteria, and their presence in this sample illustrate that it is not unusual to recover viable microbes at extreme altitudes. Additionally, the extended period required to initiate growth demonstrates the need for lengthy incubation periods when analyzing high-altitude samples for cultivable microorganisms.

Aerobiologia

Presence of amphibian chytrid fungus (Batrachochytrium dendrobatidis) in rainwater suggests aerial dispersal is possible

Abstract Global spread of the pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) may involve dispersal mechanisms not previously explored. Weather systems accompanied by strong wind and rainfall have been known to assist the dispersal of microbes pathogenic to plants and animals, and we considered a similar phenomenon might occur with Bd. We investigated this concept by sampling rainwater from 20 precipitation events for the presence of Bd in Cusuco National Park, Honduras: a site where high Bd prevalence was previously detected in stream-associated amphibians. Quantitative PCR analysis confirmed the presence of Bd in rainwater in one (5 %) of the weather events sampled, although viability cannot be ascertained from molecular presence alone. The source of the Bd and distance that the contaminated rainwater traveled could not be determined; however, this collection site was located approximately 600 m from the nearest observed perennial river by straight-line aerial distance. Although our results suggest atmospheric Bd dispersal is uncommon and unpredictable, even occasional short-distance aerial transport could considerably expand the taxonomic diversity of amphibians vulnerable to exposure and at risk of decline, including terrestrial and arboreal species that are not associated with permanent water bodies.

Aerobiologia

Summer nitrate uptake and denitrification in an upper Mississippi River backwater lake: The role of rooted aquatic vegetation

In-stream nitrogen processing in the Mississippi River has been suggested as one mechanism to reduce coastal eutrophication in the Gulf of Mexico. Aquatic macrophytes in river channels and flood plain lakes have the potential to temporarily remove large quantities of nitrogen through assimilation both by themselves and by the attached epiphyton. In addition, rooted macrophytes act as oxygen pumps, creating aerobic microsites around their roots where coupled nitrification–denitrification can occur. We used in situ 15 N–NO 3 − tracer mesocosm experiments to measure nitrate assimilation rates for macrophytes, epiphyton, and microbial fauna in the sediment in Third Lake, a backwater lake of the upper Mississippi River during June and July 2005. We measured assimilation over a range of nitrate concentrations and estimated a nitrate mass balance for Third Lake. Macrophytes assimilated the most nitrate (29.5 mg N m −2 d −1 ) followed by sediment microbes (14.4 mg N m −2 d −1 ) and epiphytes (5.7 mg N m −2 d −1 ) . Assimilation accounted for 6.8% in June and 18.6% in July of total nitrate loss in the control chambers. However, denitrification (292.4 mg N m −2 d −1 ) is estimated to account for the majority (82%) of the nitrate loss. Assimilation and denitrification rates generally increased with increasing nitrate concentration but denitrification rates plateaued at about 5 mg N L −1 . This suggests that backwaters have the potential to remove a relatively high amount of nitrate but will likely become saturated if the load becomes too large.

Iowa, Illinois, Missouri, Minnesota, Wisconsin

A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning

As the earth system changes in response to human activities, a critical objective is to predict how biogeochemical process rates (e.g. nitrification, decomposition) and ecosystem function (e.g. net ecosystem productivity) will change under future conditions. A particular challenge is that the microbial communities that drive many of these processes are capable of adapting to environmental change in ways that alter ecosystem functioning. Despite evidence that microbes can adapt to temperature, precipitation regimes, and redox fluctuations, microbial communities are typically not optimally adapted to their local environment. For example, temperature optima for growth and enzyme activity are often greater than in situ temperatures in their environment. Here we discuss fundamental constraints on microbial adaptation and suggest specific environments where microbial adaptation to climate change (or lack thereof) is most likely to alter ecosystem functioning. Our framework is based on two principal assumptions. First, there are fundamental ecological trade-offs in microbial community traits that occur across environmental gradients (in time and space). These trade-offs result in shifting of microbial function (e.g. ability to take up resources at low temperature) in response to adaptation of another trait (e.g. limiting maintenance respiration at high temperature). Second, the mechanism and level of microbial community adaptation to changing environmental parameters is a function of the potential rate of change in community composition relative to the rate of environmental change. Together, this framework provides a basis for developing testable predictions about how the rate and degree of microbial adaptation to climate change will alter biogeochemical processes in aquatic and terrestrial ecosystems across the planet.

Biogeochemistry

Unraveling mechnisms underlying effects of wetting–drying cycles on soil respiration in a dryland

Rewetting of dry soils usually stimulates soil carbon (C) emission, a phenomenon known as the Birch effect. Soil C cycling in drylands, which store approximately one third of terrestrial soil organic C (SOC), is strongly affected by wetting–drying cycles. However, the physical, chemical, and biological mechanisms that link rewetting cycles with dryland soil C cycling have not been comprehensively studied, nor do we understand how these mechanisms interact with each other. Here, we conducted a dryland soil incubation experiment manipulating four factors related to global change (soil moisture content, soil moisture variability, C availability, and prior warming) in a factorial design. The experiment was divided into two periods: a rewetting period consisting of six 14-d wetting–drying cycles; and a recovery period lasting 28 days during which soil moisture content was held stable, allowing for examination of the legacy effects of the wet-dry cycles. Rewetting cycles decreased soil aggregate stability under some conditions, but their effects on soil microbial biomass and fungal communities, soil enzyme activities, soil priming, and soil dissolved C were not significant. We found lower average soil respiration under the wetting–drying treatment than the stable soil moisture treatment, and Birch effects were observed, but only under some conditions. This was probably because moisture variability exacerbated soil microbial metabolic stress, which showed itself as oxygen limitation during the initial precipitation pulse and as water limitation during soil drying. Notably, respiration rates remained low even after moisture fluctuations ceased, suggesting a legacy effect of rewetting cycles on dryland microbial communities. Overall, rewetting inhibited aggregate formation (physical mechanism), and suppressed soil respiration by inducing soil microbial metabolic stress (biological mechanism), ultimately leading to lower soil C loss under rewetting. Our findings indicate that Birch effects are mediated by the magnitude of moisture variability, the availability of C, and the degree of physiological stress microbes experience.

Biogeochemistry

The biogeochemistry of anchialine caves: Progress and possibilities

Recent investigations of anchialine caves and sinkholes have identified complex food webs dependent on detrital and, in some cases, chemosynthetically produced organic matter. Chemosynthetic microbes in anchialine systems obtain energy from reduced compounds produced during organic matter degradation (e.g., sulfide, ammonium, and methane), similar to what occurs in deep ocean cold seeps and mud volcanoes, but distinct from dominant processes operating at hydrothermal vents and sulfurous mineral caves where the primary energy source is mantle derived. This review includes case studies from both anchialine and non-anchialine habitats, where evidence for in situ chemosynthetic production of organic matter and its subsequent transfer to higher trophic level metazoans is documented. The energy sources and pathways identified are synthesized to develop conceptual models for elemental cycles and energy cascades that occur within oligotrophic and eutrophic anchialine caves. Strategies and techniques for testing the hypothesis of chemosynthesis as an active process in anchialine caves are also suggested.

Hydrobiologia

Functional role of an endophytic Bacillus amyloliquefaciens in enhancing growth and disease protection of invasive English ivy ( Hedera helix L. )

Background We hypothesize that invasive English ivy ( Hedera helix ) harbors endophytic microbes that promote plant growth and survival. To evaluate this hypothesis, we examined endophytic bacteria in English ivy and evaluated effects on the host plant. Methods Endophytic bacteria were isolated from multiple populations of English ivy in New Brunswick, NJ. Bacteria were identified as a single species Bacillus amyloliquefaciens . One strain of B. amyloliquefaciens , strain C6c, was characterized for indoleacetic acid (IAA) production, secretion of hydrolytic enzymes, phosphate solubilization, and antibiosis against pathogens. PCR was used to amplify lipopeptide genes and their secretion into culture media was detected by MALDI-TOF mass spectrometry. Capability to promote growth of English ivy was evaluated in greenhouse experiments. The capacity of C6c to protect plants from disease was evaluated by exposing B+ (bacterium inoculated) and B− (non-inoculated) plants to the necrotrophic pathogen Alternaria tenuissima . Results B. amyloliquefaciens C6c systemically colonized leaves, petioles, and seeds of English ivy. C6c synthesized IAA and inhibited plant pathogens. MALDI-TOF mass spectrometry analysis revealed secretion of antifungal lipopeptides surfactin, iturin, bacillomycin, and fengycin. C6c promoted the growth of English ivy in low and high soil nitrogen conditions. This endophytic bacterium efficiently controlled disease caused by Alternaria tenuissima . Conclusions This study suggests that B. amyloliquefaciens plays an important role in enhancing growth and disease protection of English ivy.

Plant and Soil

Disease protection and allelopathic interactions of seed-transmitted endophytic pseudomonads of invasive reed grass ( Phragmites australis )

Background and aims Non-native Phragmites australis (haplotype M) is an invasive grass that decreases biodiversity and produces dense stands. We hypothesized that seeds of Phragmites carry microbes that improve seedling growth, defend against pathogens and maximize capacity of seedlings to compete with other plants. Methods We isolated bacteria from seeds of Phragmites , then evaluated representatives for their capacities to become intracellular in root cells, and their effects on: 1.) germination rates and seedling growth, 2.) susceptibility to damping-off disease, and 3.) mortality and growth of competitor plant seedlings (dandelion ( Taraxacum officionale F. H. Wigg) and curly dock ( Rumex crispus L.)). Results Ten strains (of 23 total) were identified and characterized; seven were identified as Pseudomonas spp. Strains Sandy LB4 ( Pseudomonas fluorescens ) and West 9 ( Pseudomonas sp.) entered root meristems and became intracellular. These bacteria improved seed germination in Phragmites and increased seedling root branching in Poa annua . They increased plant growth and protected plants from damping off disease. Sandy LB4 increased mortality and reduced growth rates in seedlings of dandelion and curly dock. Conclusions Phragmites plants associate with endophytes to increase growth and disease resistance, and release bacteria into the soil to create an environment that is favorable to their seedlings and less favorable to competitor plants.

Plant and Soil

Biodegradation of PAHs and PCBs in soils and sludges

Results from a multi-year, pilot-scale land treatment project for PAHs and PCBs biodegradation were evaluated. A mathematical model, capable of describing sorption, sequestration, and biodegradation in soil/water systems, is applied to interpret the efficacy of a sequential active-passive biotreatment process of organic chemicals on remediation sites. To account for the recalcitrance of PAHs and PCBs in soils and sludges during long-term biotreatment, this model comprises a kinetic equation for organic chemical intraparticle sequestration process. Model responses were verified by comparison to measurements of biodegradation of PAHs and PCBs in land treatment units; a favorable match was found between them. Model simulations were performed to predict on-going biodegradation behavior of PAHs and PCBs in land treatment units. Simulation results indicate that complete biostabilization will be achieved when the concentration of reversibly sorbed chemical (S RA) reduces to undetectable levels, with a certain amount of irreversibly sequestrated residual chemical (S IA) remaining within the soil particle solid phase. The residual fraction (S IA) tends to lose its original chemical and biological activity, and hence, is much less available, toxic, and mobile than the "free" compounds. Therefore, little or no PAHs and PCBs will leach from the treatment site and constitutes no threat to human health or the environment. Biotreatment of PAHs and PCBs can be terminated accordingly. Results from the pilot-scale testing data and model calculations also suggest that a significant fraction (10-30%) of high-molecular-weight PAHs and PCBs could be sequestrated and become unavailable for biodegradation. Bioavailability (large K d , i.e., slow desorption rate) is the key factor limiting the PAHs degradation. However, both bioavailability and bioactivity (K in Monod kinetics, i.e., number of microbes, nutrients, and electron acceptor, etc.) regulate PCBs biodegradation. The sequential active-passive biotreatment can be a cost-effective approach for remediation of highly hydrophobic organic contaminants. The mathematical model proposed here would be useful in the design and operation of such organic chemical biodegradation processes on remediation sites. ?? 2007 Springer Science+Business Media B.V.

Water, Air, & Soil Pollution

Aliphatic structure of humic acids; a clue to their origin

Nuclear magnetic resonance spectra (both 1 H and 13 C) of humic acids from diverse depositional environments indicate the presence of aromatic chemical structures, most likely derived from lignin of vascular plants, and complex, paraffinic structures, most likely derived from algal or microbial sources. The latter components account for a major fraction of humic acid structures in both terrestrial and aquatic environments, suggesting that algae or microbes play a large role in humification of organic remains from both systems.

Organic Geochemistry

Evidence for widespread microbivory of endophytic bacteria in roots of vascularplants through oxidative degradation in root cell periplasmic spaces

In this chapter we present a hypothesis, and data supporting it, that vascular plants in diverse families possess symbiotic/endophytic bacteria that frequently vector on or within their seeds; seedlings degrade symbiotic bacteria within roots. Evidence of widespread microbivory was found in a survey for intracellular bacteria that we conducted including seedlings in 36 species of vascular plants distributed in 20 plant families. Experiments indicate that when seeds germinate, bacteria colonize seedlings and internalize into root cells where they are oxidatively-degraded in the periplasmic spaces of cells. The process of degradation of microbes in roots has been termed “rhizophagy”, and “rhizophagy cycle” or “rhizophagy symbiosis” in the case of symbiotic bacteria that alternate between a free-living soil phase and intracellular/endophytic phase. We hypothesize that microbivory could account for a significant portion of nutrients acquired by plants from soils—with one estimate suggesting that as much as 30% of the nutrients acquired by seedlings may stem from rhizophagy symbiosis. Developing a better understanding of rhizophagy symbiosis could lead to new ways to cultivate crops without reliance on excessive agrochemical applications. Learning how to manipulate rhizophagy symbiosis could result in new technologies for reducing growth of weedy or invasive plant species by inhibiting rhizophagy symbiosis.

Book chapter

Hydrogeochemistry and microbiology of mine drainage: An update

The extraction of mineral resources requires access through underground workings, or open pit operations, or through drillholes for solution mining. Additionally, mineral processing can generate large quantities of waste, including mill tailings, waste rock and refinery wastes, heap leach pads, and slag. Thus, through mining and mineral processing activities, large surface areas of sulfide minerals can be exposed to oxygen, water, and microbes, resulting in accelerated oxidation of sulfide and other minerals and the potential for the generation of low-quality drainage. The oxidation of sulfide minerals in mine wastes is accelerated by microbial catalysis of the oxidation of aqueous ferrous iron and sulfide. These reactions, particularly when combined with evaporation, can lead to extremely acidic drainage and very high concentrations of dissolved constituents. Although acid mine drainage is the most prevalent and damaging environmental concern associated with mining activities, generation of saline, basic and neutral drainage containing elevated concentrations of dissolved metals, non-metals, and metalloids has recently been recognized as a potential environmental concern. Acid neutralization reactions through the dissolution of carbonate, hydroxide, and silicate minerals and formation of secondary aluminum and ferric hydroxide phases can moderate the effects of acid generation and enhance the formation of secondary hydrated iron and aluminum minerals which may lessen the concentration of dissolved metals. Numerical models provide powerful tools for assessing impacts of these reactions on water quality.

Applied Geochemistry