Biogeochemical cycling papers Category

“Clouds are key components in Earth’s functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active  in situ  remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain’s meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members. Communities consisted of ~10³âˆ’10⁴  bacteria and archaea mL^-1and ~10²âˆ’10³  eukaryote cells mL^-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata. Within these complex communities, the active members of cloud microbiota were identified as Alpha- (Sphingomonadales, Rhodospirillales and Rhizobiales), Beta- (Burkholderiales) and Gamma-Proteobacteria (Pseudomonadales). These groups of bacteria usually classified as epiphytic are probably the best candidates for interfering with abiotic chemical processes in clouds, and the most prone to successful aerial dispersion.”

Summary:  We have long known about the microbial presence within clouds but until recently most of our data has been a result of cell culturing which as we all know: may not be representative of the microbial community. This study via the use of 16s amplicon sequencing sought to define both the taxonomic identity and microbial activity via extracted DNA and RNA respectively. Atmospheric samples were taken periodically above France via a modified weather probes. Each sample was screened for the relative amount of industrial contaminants to serve as a comparison to the negative control. This study found that on average 11000 to 21000 distinct OTUs which is comparable to that of a typical soil sample. Prokaryotes made up the majority of the sample with low amounts of eukaryotic fungal populations also being present.  The source of this diversity has been attributed to aerosols particulate products that resulted from saphorytes. The Microbial richness of the aforementioned microbes was more pronounced in the contaminated samples. Between all the samples it was evident that the metabolic functions of these microbes were important for many hydrological mechanisms such as ice nucleation and ion mediated chemistry reactions which aid in both the formation of water droplets and the act of precipitation respectively. The microbiome of the cloud was found to be variable depending on the location and sensitive to changes in resources (such as industrial contaminants, temperature and topography) so further study should be allocated to defining, and in the far future, altering the clouds’ microbiome.    

Amato P, Joly M, Besaury L, Oudart A, Taib N, Moné AI, et al. (2017) Active microorganisms thrive among extremely diverse communities in cloud water. PLoS ONE 12(8): e0182869. https://doi.org/10.1371/journal.pone.0182869

Zhao, M., Xue, K., Wang, F., Liu, S., Bai, S., Sun, B., … & Yang, Y. (2014). Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping.  The ISME journal,  8(10), 2045.

• doi:10.1038/ismej.2014.46

Abstract:

Despite microbes’ key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO₂) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO₂efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling.

I chose this paper because it looks at simulating climate changes to study how microbe biogeochemical cycles react to these changes. This paper mainly looks at the effects of southward soil cropping and maize cropping. I also thought this would be a good paper to look at because geochips were used which were recently talked about in class.

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Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur

Raina, J.B., Tapiolas, D., Willis, B.L., & D.G. Bourne. 2009. Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur. Appl. Env. Microbiology  vol. 75;11. pp3492-3501. doi:  10.1128/AEM.02567-08

Marine bacteria play a central role in the degradation of dimethylsulfoniopropionate (DMSP) to dimethyl sulfide (DMS) and acrylic acid, DMS being critical to cloud formation and thereby cooling effects on the climate. High concentrations of DMSP and DMS have been reported in scleractinian coral tissues although, to date, there have been no investigations into the influence of these organic sulfur compounds on coral-associated bacteria. Two coral species,  Montipora aequituberculata  and  Acropora millepora, were sampled and their bacterial communities were characterized by both culture-dependent and molecular techniques. Four genera,  Roseobacter, Spongiobacter, Vibrio, and  Alteromonas, which were isolated on media with either DMSP or DMS as the sole carbon source, comprised the majority of clones retrieved from coral mucus and tissue 16S rRNA gene clone libraries. Clones affiliated with  Roseobacter  sp. constituted 28% of the  M. aequituberculata  tissue libraries, while 59% of the clones from the  A. millepora  libraries were affiliated with sequences related to the  Spongiobacter  genus.  Vibrio  spp. were commonly isolated from DMS and acrylic acid enrichments and were also present in 16S rRNA gene libraries from coral mucus, suggesting that under “normal’ environmental conditions, they are a natural component of coral-associated communities. Genes homologous to  dddD, and  dddL, previously implicated in DMSP degradation, were also characterized from isolated strains, confirming that bacteria associated with corals have the potential to metabolize this sulfur compound when present in coral tissues. Our results demonstrate that DMSP, DMS, and acrylic acid potentially act as nutrient sources for coral-associated bacteria and that these sulfur compounds are likely to play a role in structuring bacterial communities in corals, with important consequences for the health of both corals and coral reef ecosystems.

I chose this article because of the diversity of microbial analysis methods used in the paper: 16S rRNA amplicon sequencing, traditional culturing, and functional gene amplicon sequencing. In addition, Im very interested in the implications of coral-associated DMS producing bacteria and their affect on climate change, especially given the recent bleaching and mass die off events in teh Great Barrier Reef.

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Website:  https://eds.b.ebscohost.com/eds/detail/detail?vid=4&sid=a5e4c708-5b7f-4d1b-83d3-16b1b176d732%40sessionmgr104&bdata=JnNpdGU9ZWRzLWxpdmU%3d#AN=S0031018212003598&db=edselp

Citation: Pfeiffer, Mirjam, J. van Leeuwen, W. O. van der Knap, and J. O. Kaplan. The effect of abrupt climatic warming on biogeochemical cycling and N2O emissions in a terrestrial ecosystem. 2012. Early Rapid Warning. 391: 74-83.

Abstract:  The large, rapid increase in atmospheric N₂O concentrations that occurred concurrent with the abrupt warming at the end of the Last Glacial period might have been the result of a reorganization in global biogeochemical cycles. To explore the sensitivity of nitrogen cycling in terrestrial ecosystems to abrupt warming, we combined a scenario of climate and vegetation composition change based on multiproxy data for the Oldest Dryas—Bølling abrupt warming event at Gerzensee, Switzerland, with a biogeochemical model that simulates terrestrial N uptake and release, including N₂O emissions. As for many central European sites, the pollen record at the Gerzensee is remarkable for the abundant presence of the symbiotic nitrogen fixer Hippophaë rhamnoides (L.) during the abrupt warming that also marks the beginning of primary succession on immature glacial soils. Here we show that without additional nitrogen fixation, climate change results in a significant increase of N₂O emissions of approximately factor 3.4 (from 6.4 ±1.9 to 21.6 ±5.9mgN₂O—Nm^−2yr^−1). Each additional 1000mgm^−2yr^−1 of nitrogen added to the ecosystem through N-fixation results in additional N₂O emissions of 1.6mgN₂O—Nm^−2yr^−1 for the time with maximum H. rhamnoides coverage. Our results suggest that local reactions of emissions to abrupt climate change could have been considerably faster than the overall atmospheric concentration changes observed in polar ice. Nitrogen enrichment of soils due to the presence of symbiotic N-fixers during early primary succession not only facilitates the establishment of vegetation on soils in their initial stage of development, but can also have considerable influence on biogeochemical cycles and the release of reactive nitrogen trace gases to the atmosphere.

Justification: I chose this article because I want to learn more about chemical emissions into the environment/certain ecosystems. What spiked this interest was first discovering that methane could actually form bubbles under the ice (people have been known to even pop them) and methane is being released into colder environments from permafrost thawing. I want to learn about what other chemicals are being released and what harm or good this is doing.

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https://onlinelibrary.wiley.com.proxy.library.uaf.edu/doi/10.1890/090220/full

Coupling biogeochemical cycles in urban environments: ecosystem services, green solutions, and misconceptions

Abstract

“Urban green space is purported to offset greenhouse-gas (GHG) emissions, remove air and water pollutants, cool local climate, and improve public health. To use these services, municipalities have focused efforts on designing and implementing ecosystem-services-based “green infrastructure’ in urban environments. In some cases the environmental benefits of this infrastructure have been well documented, but they are often unclear, unquantified, and/or outweighed by potential costs. Quantifying biogeochemical processes in urban green infrastructure can improve our understanding of urban ecosystem services and disservices (negative or unintended consequences) resulting from designed urban green spaces. Here we propose a framework to integrate biogeochemical processes into designing, implementing, and evaluating the net effectiveness of green infrastructure, and provide examples for GHG mitigation, stormwater runoff mitigation, and improvements in air quality and health.”

This article discuses how ‘green infrastructure’ can be both psychologically and environmentally beneficial, and can be utilized as a food source.  The article focuses on the water cycling and nutrient cycling that a green infrastructure needs to be sustainable, and any organic matter that can help mitigate effects of greenhouse gases.

Citation:
Pataki, D. E., Carreiro, M. M., Cherrier, J., Grulke, N. E., Jennings, V., Pincetl, S., Pouyat, R. V., Whitlow, T. H. and Zipperer, W. C. (2011), Coupling biogeochemical cycles in urban environments: ecosystem services, green solutions, and misconceptions. Frontiers in Ecology and the Environment, 9: 27—36. doi:10.1890/090220

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https://www.sciencedirect.com/science/article/pii/0016703780900459

Martens, C., J. Val Klump. 1979. Biogeochemical cycling in an organic-rich coastal marine basin-I. Methane sediment-water exchange processes. Elsevier 44:471-490.

I chose this article because I was very interested in seeing how methane affects the earth, especially since it is being released more and more due to the thawing of permafrost. I was also very intrigued when we learned about the frozen methane bubbles in the lakes during one of our earlier lectures. After learning a little bit about methane in cold environments, such as Fairbanks, I thought it would be interesting to compare it to a warmer environment which this article does. It takes a look at how methane is produced through different mechanisms in bodies of water in North Carolina. I thought this would be interesting because the temperature changes in North Carolina aren’t nearly as extreme and the changes in Fairbanks, so I was interested in learning if the difference in temperature made a difference.

Abstract

Methane produced in anoxic organic-rich sediments of Cape Lookout Bight, North Carolina, enters the water column via two seasonally dependent mechanisms: diffusion and bubble ebullition. Diffusive transport measured  in situ  with benthic chambers averages 49 and 163 μmol · m  ^−2   · hr  ^−1  during November—May and June—October respectively. High summer sediment methane production causes saturation concentrations and formation of bubbles near the sediment-water interface. Subsequent bubble ebullition is triggered by low-tide hydrostatic pressure release. June—October sediment-water gas fluxes at the surface average 411 ml (377 ml STP: 16.8 mmol) · m^−2  per low tide. Bubbling maintains open bubble tubes which apparently enhance diffusive transport. When tubes are present, apparent sediment diffusivities are 1.2—3.1-fold higher than theoretical molecular values reaching a peak value of 5.2 × 10^−5  cm²   · sec^−1. Dissolution of 15% of the rising bubble flux containing 86% methane supplies 170μmol · m^−2   · hr^−1  of methane to the bight water column during summer months; the remainder is lost to the troposphere. Bottom water methane concentration increases observed during bubbling can be predicted using a 5—15 μm stagnant boundary layer dissolution model. Advective transport to surrounding waters is the major dissolved methane sink: aerobic oxidation and diffusive atmospheric evasion losses are minor within the bight.

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Nazaries, L., Pan, Y., Bodrossy, L., Baggs, E. M., Millard, P., Murrell, J. C., & Singh, B. K. (2013). Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change.  Applied and Environmental Microbiology,  79(13), 4031—4040. https://doi.org/10.1128/AEM.00095-13

https://aem.asm.org/content/79/13/4031.full

Abstract:  Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles.

Justification: This paper is very relevant to what we’ve been discussing in class, as well as issues scientists are facing today. It explores how microbial communities fluctuate based on changes in their environment, specifically looking at how biogeochemical processes are influenced.