Temperature sensitivity of biomass‐specific microbial exo‐enzyme activities and CO2 efflux is resistant to change across short‐ and long‐term timescales

Accurate representation of temperature sensitivity (Q₁₀) of soil microbial activity across time is critical for projecting soil CO₂ efflux. As microorganisms mediate soil carbon (C) loss via exo‐enzyme activity and respiration, we explore temperature sensitivities of microbial exo‐enzyme activity and respiratory CO₂ loss across time and assess mechanisms associated with these potential changes in microbial temperature responses. We collected soils along a latitudinal boreal forest transect with different temperature regimes (long‐term timescale) and exposed these soils to laboratory temperature manipulations at 5, 15, and 25°C for 84 days (short‐term timescale). We quantified temperature sensitivity of microbial activity per g soil and per g microbial biomass at days 9, 34, 55, and 84, and determined bacterial and fungal community structure before the incubation and at days 9 and 84. All biomass‐specific rates exhibited temperature sensitivities resistant to change across short‐ and long‐term timescales (mean Q₁₀ = 2.77 ± 0.25, 2.63 ± 0.26, 1.78 ± 0.26, 2.27 ± 0.25, 3.28 ± 0.44, 2.89 ± 0.55 for β‐glucosidase, N‐acetyl‐β‐d ‐glucosaminidase, leucine amino peptidase, acid phosphatase, cellobiohydrolase, and CO₂ efflux, respectively). In contrast, temperature sensitivity of soil mass‐specific rates exhibited either resilience (the Q₁₀ value changed and returned to the original value over time) or resistance to change. Regardless of the microbial flux responses, bacterial and fungal community structure was susceptible to change with temperature, significantly differing with short‐ and long‐term exposure to different temperature regimes. Our results highlight that temperature responses of microbial resource allocation to exo‐enzyme production and associated respiratory CO₂ loss per unit biomass can remain invariant across time, and thus, that vulnerability of soil organic C stocks to rising temperatures may persist in the long term. Furthermore, resistant temperature sensitivities of biomass‐specific rates in spite of different community structures imply decoupling of community constituents and the temperature responses of soil microbial activities.     

Revival of the biological sunlight‐to‐biogas energy conversion system

In the quest for renewable resources, algae are increasingly receiving attention. Their high growth rate, high CO₂ fixation and their lack of requirement for fertile soil surface represent several advantages as compared to conventional (energy) crops. Through their ability to store large amounts of oils, they qualify as a source for biodiesel. Algal biomass, however, can also be used as such, namely as a substrate for anaerobic digestion. In the present research, we investigated the use of algae for energy generation in a stand‐alone, closed‐loop system. The system encompasses an algal growth unit for biomass production, an anaerobic digestion unit to convert the biomass to biogas and a microbial fuel cell to polish the effluent of the digester. Nutrients set free during digestion can accordingly be returned to the algal growth unit for a sustained algal growth. Hence, a system is presented that continuously transforms solar energy into energy‐rich biogas and electricity. Algal productivities of 24–30 ton VS ha^?1 year^?1 were reached, while 0.5 N m³ biogas could be produced kg^?1 algal VS. The system described resulted in a power plant with a potential capacity of about 9 kW ha^?1 of solar algal panel, with prospects of 23 kW ha^?1. Biotechnol. Bioeng. 2009;103: 296–304. © 2009 Wiley Periodicals, Inc.     

The kinetics of siderophore‐mediated olivine dissolution

Silicate minerals represent an important reservoir of nutrients at Earth's surface and a source of alkalinity that modulates long‐term geochemical cycles. Due to the slow kinetics of primary silicate mineral dissolution and the potential for nutrient immobilization by secondary mineral precipitation, the bioavailability of many silicate‐bound nutrients may be limited by the ability of micro‐organisms to actively scavenge these nutrients via redox alteration and/or organic ligand production. In this study, we use targeted laboratory experiments with olivine and the siderophore deferoxamine B to explore how microbial ligands affect nutrient (Fe) release and the overall rate of mineral dissolution. Our results show that olivine dissolution rates are accelerated in the presence of micromolar concentrations of deferoxamine B. Based on the non‐linear decrease in rates with time and formation of a Fe³⁺‐ligand complex, we attribute this acceleration in dissolution rates to the removal of an oxidized surface coating that forms during the dissolution of olivine at circum‐neutral pH in the presence of O₂ and the absence of organic ligands. While increases in dissolution rates are observed with micromolar concentrations of siderophores, it remains unclear whether such conditions could be realized in natural environments due to the strong physiological control on microbial siderophore production. So, to contextualize our experimental results, we also developed a feedback model, which considers how microbial physiology and ligand‐promoted mineral dissolution kinetics interact to control the extent of biotic enhancement of dissolution rates expected for different environments. The model predicts that physiological feedbacks severely limit the extent to which dissolution rates may be enhanced by microbial activity, though the rate of physical transport modulates this limitation.     

Above‐ and belowground linkages in Sphagnum peatland: climate warming affects plant‐microbial interactions

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above‐ and belowground linkages that regulate soil organic carbon dynamics and C‐balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top‐predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum‐polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above‐ and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands     

T‐RFLP reveals high β‐Proteobacteria diversity in microbial fuel cells enriched with domestic wastewater

Aims: To assess the biodiversity of a large number of microbial fuel cell (MFC) anodes from a variety of MFC designs, all enriched with domestic wastewater, using a molecular fingerprinting method. Methods and Results: We optimized a protocol allowing the rapid characterization of MFC communities using terminal restriction fragment length polymorphism (T‐RFLP) with two different sets of primers and a varying number of restriction enzymes. This protocol was further validated by direct comparison with bacterial clone libraries. Twenty‐one MFC anodes were analysed by T‐RFLP. We also provided a statistical comparison with other bacterial communities from environments sharing common features. Conclusions: Bacterial communities were dominated by β‐Proteobacteria, mostly belonging to the Burkholderiales order, that are known to play an active role in the cycle of metals such as iron and manganese. This property may allow them to properly pass electrons to the anode of an MFC. Significance and Impact of the Study: Unlike other groups, β‐Proteobacteria have seldom been acknowledged as potentially efficient electrochemically active bacteria (EAB) in MFCs. Yet, they are plentiful in natural environments like biocorrosion biofilms and acid mine drainages that consequently show some potential for MFC enrichment.     

GeoChip 4: a functional gene‐array‐based high‐throughput environmental technology for microbial community analysis

Micro‐organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro‐organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82 000 probes covering 141 995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro‐organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500 ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long‐term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long‐term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.     

High‐throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil‐drilling activities

As global exploitation of available resources increases, operations extend towards sensitive and previously protected ecosystems. It is important to monitor such areas in order to detect, understand and remediate environmental responses to stressors. The natural heterogeneity and complexity of communities means that accurate monitoring requires high resolution, both temporally and spatially, as well as more complete assessments of taxa. Increased resolution and taxonomic coverage is economically challenging using current microscopy‐based monitoring practices. Alternatively, DNA sequencing‐based methods have been suggested for cost‐efficient monitoring, offering additional insights into ecosystem function and disturbance. Here, we applied DNA metabarcoding of eukaryotic communities in marine sediments, in areas of offshore drilling on the Norwegian continental shelf. Forty‐five samples, collected from seven drilling sites in the Troll/Oseberg region, were assessed, using the small subunit ribosomal RNA gene as a taxonomic marker. In agreement with results based on classical morphology‐based monitoring, we were able to identify changes in sediment communities surrounding oil platforms. In addition to overall changes in community structure, we identified several potential indicator taxa, responding to pollutants associated with drilling fluids. These included the metazoan orders Macrodasyida, Macrostomida and Ceriantharia, as well as several ciliates and other protist taxa, typically not targeted by environmental monitoring programmes. Analysis of a co‐occurrence network to study the distribution of taxa across samples provided a framework for better understanding the impact of anthropogenic activities on the benthic food web, generating novel, testable hypotheses of trophic interactions structuring benthic communities.     

Control of microbial attachment by inhibition of ATP and ATP‐mediated autoinducer‐2

In this study, 2,4‐dinitrophenol (DNP), a typical chemical uncoupler, was employed to investigate the possible roles of ATP and autoinducer‐2 (AI‐2) of suspended microorganisms in attachment onto nylon membrane and glass slide surfaces. Results showed that DNP could disrupt ATP synthesis, subsequently led to a reduced production of AI‐2 which is a common signaling molecule for cellular communication. Attachment of suspended microorganisms exposed to DNP was significantly suppressed as compared to microorganisms without contact with DNP. These suggest that an energized state of suspended microorganisms would favor microbial attachment to both nylon membrane and glass slide surfaces. The extent of microbial attachment was found to be positively related to the AI‐2 content of microorganisms. This study offers insights into the control of biofouling by preventing initial microbial attachment through inhibition of energy metabolism. Biotechnol. Bioeng. 2010;107: 31–36. © 2010 Wiley Periodicals, Inc.     

Photo‐switchable microbial fuel‐cells

Regulation of Bio‐systems in a clean, simple, and efficient way is important for the design of smart bio‐interfaces and bioelectronic devices. Light as a non‐invasive mean to control the activity of a protein enables spatial and temporal control far superior to other chemical and physical methods. The ability to regulate the activity of a catalytic enzyme in a biofuel‐cell reduces the waste of resources and energy and turns the fuel‐cell into a smart and more efficient device for power generation. Here we present a microbial‐fuel‐cell based on a surface displayed, photo‐switchable alcohol dehydrogenase. The enzyme was modified near the active site using non‐canonical amino acids and a small photo‐reactive molecule, which enables reversible control of enzymatic activity. Depending on the modification site, the enzyme exhibits reversible behavior upon irradiation with UV and visible light, in both biochemical, and electrochemical assays. The change observed in power output of a microbial fuel cell utilizing the modified enzyme was almost five‐fold, between inactive and active states.     

Co‐utilization of acidified glycerol pretreated‐sugarcane bagasse for microbial oil production by a novel Rhodosporidium strain

Acidified glycerol pretreatment is very effective to deconstruct lignocellulosics for producing glucose. Co‐utilization of pretreated biomass and residual glycerol to bioproducts could reduce the costs associated with biomass wash and solvent recovery. In this study, a novel strain Rhodosporidium toruloides RP 15, isolated from sugarcane bagasse, was selected and tested for coconversion of pretreated biomass and residual glycerol to microbial oils. In the screening trails, Rh. toruloides RP 15 demonstrated the highest oil production capacity on glucose, xylose, and glycerol among the 10 strains. At the optimal C:N molar ratio of 140:1, this strain accumulated 56.7, 38.3, and 54.7% microbial oils based on dry cell biomass with 30 g/L glucose, xylose, and glycerol, respectively. Furthermore, sugarcane bagasse medium containing 32.6 g/L glucose from glycerol‐pretreated bagasse and 23.4 g/L glycerol from pretreatment hydrolysate were used to produce microbial oils by Rh. toruloides RP 15. Under the preliminary conditions without pH control, this strain produced 7.7 g/L oil with an oil content of 59.8%, which was comparable or better than those achieved with a synthetic medium. In addition, this strain also produced 3.5 mg/L carotenoid as a by‐product. It is expected that microbial oil production can be significantly improved through process optimization.     

Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate

Aims

The aim of the study was to develop an approach to enrich ionic liquid tolerant micro‐organisms that efficiently decompose lignocellulose in a thermophilic and high‐solids environment.

Methods and Results

High‐solids incubations were conducted, using compost as an inoculum source, to enrich for thermophilic communities that decompose switchgrass in the presence of the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate ([C2mim][OAc]). Ionic liquid levels were increased from 0 to 6% on a total weight basis incrementally. Successful enrichment of a community that decomposed lignocellulose at 55°C in the presence of 6% [C2mim][OAc] was achieved, when the [C2mim][OAc] level was increased stepwise from 2% to 4% to 5% to 6%. Pyrosequencing results revealed a shift in the community and a sharp decrease in richness, when thermophilic conditions were applied.

Conclusions

A community tolerant to a thermophilic, high‐solids environment containing 6% [C2mim][OAc] was enriched from compost. Gradually increasing [C2mim][OAc] concentrations allowed the community to adapt to [C2mim][OAc].

Significance and Impact of the Study

A successful approach to enrich communities that decompose lignocellulose under thermophilic high‐solids conditions in the presence of elevated levels of [C2mim][OAc] has been developed. Communities yielded from this approach will provide resources for the discovery of enzymes and metabolic pathways relevant to biomass pretreatment and fuel production.     

Bacterial community succession in a high‐altitude subarctic glacier foreland is a three‐stage process

Alpine glaciers are retreating rapidly, exposing foreland minerals, which develop into soils. Bacterial communities in glacier forelands exhibit high rates of turnover and undergo dramatic shifts in composition within the first 50 years after deglaciation, followed by relative stabilization and convergence. This period of microbial development occurs simultaneously with plant colonization in most systems; thus, it remains unclear whether the changes in the bacterial communities occur primarily as the result of edaphic, climatic or biotic factors. We examined bacterial community structure along two replicate chronosequences within the glacial foreland of Duke River Glacier, Yukon, Canada. This foreland is estimated to include >200 years of bare soils before an appreciable grassline, likely due to the high latitude and altitude of the glacier. This enabled us to examine bacterial community development prior to plant colonization over a longer period than previous studies. We observed three successional groups in the chronosequence: (i) an ‘early’ group in soils of less than approximately 50 years since deglaciation; (ii) an ‘intermediate’ group within bare soils, after the early period but before the grassline, containing communities with a relatively high degree of variability in composition; and (iii) a ‘grassline’ group in soils collected after plant colonization with higher diversity but lower age‐group variability in community composition. These findings suggest rapid replacement and addition of species better adapted to glacier foreland conditions followed by slower community shifts over the next 150 years and, finally, indications of a possible response to plant colonization.     

Effects of forest degradation on microbial communities and soil carbon cycling: A global meta‐analysis

Aim

The aim was to explore how conversions of primary or secondary forests to plantations or agricultural systems influence soil microbial communities and soil carbon (C) cycling.

Location

Global.

Time period

1993–2017.

Major taxa studied

Soil microbes.

Methods

A meta‐analysis was conducted to examine effects of forest degradation on soil properties and microbial attributes related to microbial biomass, activity, community composition and diversity based on 408 cases from 119 studies in the world.

Results

Forest degradation decreased the ratios of K‐strategists to r‐strategists (i.e., ratios of fungi to bacteria, Acidobacteria to Proteobacteria, Actinobacteria to Bacteroidetes and Acidobacteria + Actinobacteria to Proteobacteria + Bacteroidetes). The response ratios (RRs) of the K‐strategist to r‐strategist ratios to forest degradation decreased and increased with increased RRs of soil pH and soil C to nitrogen ratio (C:N), respectively. Forest degradation increased the bacterial alpha‐diversity indexes, of which the RRs increased and decreased as the RRs of soil pH and soil C:N increased, respectively. The overall RRs across all the forest degradation types ranked as microbial C (?40.4%) > soil C (?33.3%) > microbial respiration (?18.9%) > microbial C to soil C ratio (qMBC; ?15.9%), leading to the RRs of microbial respiration rate per unit microbial C (qCO₂) and soil C decomposition rate (respiration rate per unit soil C), on average, increasing by +43.2 and +25.0%, respectively. Variances of the RRs of qMBC and qCO₂ were significantly explained by the soil C, soil C:N and mean annual precipitation.

Main conclusions

Forest degradation consistently shifted soil microbial community compositions from K‐strategist dominated to r‐strategist dominated, altered soil properties and stimulated microbial activity and soil C decomposition. These results are important for modelling the soil C cycling under projected global land‐use changes and provide supportive evidence for applying the macroecology theory on ecosystem succession and disturbance in soil microbial ecology.     

On the biogenicity of Fe‐oxyhydroxide filaments in silicified low‐temperature hydrothermal deposits: Implications for the identification of Fe‐oxidizing bacteria in the rock record

Microaerophilic Fe(II)‐oxidizing bacteria produce biomineralized twisted and branched stalks, which are promising biosignatures of microbial Fe oxidation in ancient jaspers and iron formations. Extracellular Fe stalks retain their morphological characteristics under experimentally elevated temperatures, but the extent to which natural post‐depositional processes affect fossil integrity remains to be resolved. We examined siliceous Fe deposits from laminated mounds and chimney structures from an extinct part of the Jan Mayen Vent Fields on the Arctic Mid‐Ocean Ridge. Our aims were to determine how early seafloor diagenesis affects morphological and chemical signatures of Fe‐oxyhydroxide biomineralization and how extracellular stalks differ from abiogenic features. Optical and scanning electron microscopy in combination with focused ion beam‐transmission electron microscopy (FIB‐TEM) was used to study the filamentous textures and cross sections of individual stalks. Our results revealed directional, dendritic, and radial arrangements of biogenic twisted stalks and randomly organized networks of hollow tubes. Stalks were encrusted by concentric Fe‐oxyhydroxide laminae and silica casings. Element maps produced by energy dispersive X‐ray spectroscopy (EDS) in TEM showed variations in the content of Si, P, and S within filaments, demonstrating that successive hydrothermal fluid pulses mediate early diagenetic alteration and modify the chemical composition and surface features of stalks through Fe‐oxyhydroxide mineralization. The carbon content of the stalks was generally indistinguishable from background levels, suggesting that organic compounds were either scarce initially or lost due to percolating hydrothermal fluids. Dendrites and thicker abiotic filaments from a nearby chimney were composed of nanometer‐sized microcrystalline iron particles and silica and showed Fe growth bands indicative of inorganic precipitation. Our study suggests that the identification of fossil stalks and sheaths of Fe‐oxidizing bacteria in hydrothermal paleoenvironments may not rely on the detection of organic carbon and demonstrates that abiogenic filaments differ from stalks and sheaths of Fe‐oxidizing bacteria with respect to width distribution, ultrastructure, and textural context.