Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples

Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities

Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.

Photo-produced aromatic compounds stimulate microbial degradation of dissolved organic carbon in thermokarst lakes

Photochemical and biological degradation of dissolved organic carbon (DOC) and their interactions jointly contribute to the carbon dioxide released from surface waters in permafrost regions. However, the mechanisms that govern the coupled photochemical and biological degradation of DOC are still poorly understood in thermokarst lakes. Here, by combining Fourier transform ion cyclotron resonance mass spectrometry and microbial high-throughput sequencing, we conducted a sunlight and microbial degradation experiment using water samples collected from 10 thermokarst lakes along a 1100-km permafrost transect. We demonstrate that the enhancement of sunlight on DOC biodegradation is not associated with the low molecular weight aliphatics produced by sunlight, but driven by the photo-produced aromatics. This aromatic compound-driven acceleration of biodegradation may be attributed to the potential high abilities of the microbes to decompose complex compounds in thermokarst lakes. These findings highlight the importance of aromatics in regulating the sunlight effects on DOC biodegradation in permafrost-affected lakes.

Exploring the mechanism of a novel recirculating aquaculture system based on water quality parameters and bacterial communities

To mitigate the serious environmental problems caused by aquaculture wastewater discharge, the development of improved aquaculture systems with more self-purification capacity and less environmental impact has become essential. A novel recirculating aquaculture system (RAS) with ecological ponds was introduced. However, the mechanism of how the ecological ponds decompose the nutrients from the residual feed and excrement of fish is still unclear. Therefore, we designed a seven-week field experiment to explore the dynamic of water quality and the shift of bacterial communities during the initial stage of the RAS ecosystem to maintain the stability of the system. According to the result, the dissolved oxygen concentration maintained at 5.63 to 10.22 mg·L^-1 in aquaculture water, and electrical conductivity increased by 100% to over 800 μs·cm^-1. High-throughput sequencing showed that the abundance and diversity of the bacterial communities in sediment samples were significantly higher than in water samples, and the Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria were dominant phyla in all samples. The relative abundance of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and nitrite-oxidizing bacteria was lower than 0.10, but rising. Redundancy analysis suggested that TOC, EC, NO₃^-, and NO₂^- were the most important factors shaping the bacterial communities in aquaculture water. Our studies assessed the RAS with ecological ponds for the first time based on water quality parameters and bacterial communities, which indicates that decomposition capacity is insufficient but improved at the initial stage of the operation, and potential risks like eutrophication require attention.

Storage of soil microbiome for application in sustainable agriculture: prospects and challenges

Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as "next-generation biologicals" for future applications via soil transplantation. The challenge, therefore, is to devise a strategy for the storage of soil microbiome such that its "functionality" is preserved for later application. This review discusses the current endeavours made towards storage of the soil microbiome. The methods for assessing the integrity of soil microbiome by targeting the structural diversity and functional potential of the preserved microbiomes have also been discussed. Further, the success stories related to the storage of fecal microbiome for application in transplants have also been highlighted. This is done primarily with the objective of learning lessons, and parallel application of the knowledge gained, in bringing about improvement in the research domain of soil microbiome storage. Subsequently, the limitations of current techniques of preservation have also been delineated. Further, the open questions in the area have been critically discussed. In conclusion, possible alternatives for storage, comprehensive analyses of the composition of the stored microbiome and their potential have been presented.

Soil Sample Preservation Strategy Affects the Microbial Community Structure

Sample preservation is a critical procedure in any research that relies on molecular tools and is conducted in remote areas. Sample preservation options include low and room temperature storage, which require freezing equipment and specific buffering solutions, respectively. The aim of the present study was to investigate whether DNA/RNA Shield 1x from Zymo Research and DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution performed similarly to snap freezing in liquid nitrogen. Soil samples were stored for 1 month in each of the buffers and without any solution at a range of temperatures: –20, +4, and +23°C. All treatments were compared to the “optimal treatment”, namely, snap freezing in liquid nitrogen. The quality and quantity of DNA were analyzed, and the microbial community structure was investigated in all samples. The results obtained indicated that the quantity and integrity of DNA was preserved well in all samples; however, the taxonomic distribution was skewed in samples stored without any solution at ambient temperatures, particularly when analyses were performed at lower taxonomic levels. Although both solutions performed equally well, sequencing output and OTU numbers in DESS-treated samples were closer to those snap frozen with liquid nitrogen. Furthermore, DNA/RNA Shield-stored samples performed better for the preservation of rare taxa.

Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results

With the advances of sequencing tools, the fields of environmental microbiology and soil ecology have been transformed. Today, the unculturable majority of soil microbes can be sequenced. Although these tools give us tremendous power and open many doors to answer important questions, we must understand how sample processing may impact our results and interpretations. Here, we test the impacts of four soil storage methods on downstream amplicon metabarcoding and qPCR analyses for fungi and bacteria. We further investigate the impact of thaw time on extracted DNA to determine a safe length of time during which this can occur with minimal impact on study results. Overall, we find that storage using standard cold packs with subsequent storage at -20°C is little different than immediate storage in liquid nitrogen, suggesting that the historical and current method is adequate. We further find evidence that storage at room temperature or with aid of RNAlater can lead to changes in community composition and in the case of RNAlater, lower gene copies. We therefore advise against these storage methods for metabarcoding analyses. Finally, we show that over 1 month, DNA extract thaw time does not impact diversity or qPCR metrics. We hope that this work will help researchers working with soil bacteria and fungi make informed decisions about soil storage and transport to ensure repeatability and accuracy of results and interpretations.

Comparative analysis of microbial community structure in the ponds with different aquaculture model and fish by high-throughput sequencing

The pond has a complex microbial ecosystem, including microorganisms in water and sediment, which plays an important role in the health of fish and water quality. The microbial community structure in the ponds can be easily affected by many factors. However, not much is known about the role of different aquaculture model and fish on the microbial community structure in ponds. The purpose of the study was to investigate the microbial diversity and composition of the ponds with different aquaculture model and fish by high-throughput sequencing. A total of 3835072 valid sequences were achieved from 60 samples. Additionally, 2064 and 1917 core OTUs were observed in water and sediment samples, respectively. Our results suggested that sediment samples have a higher abundance and diversity of microbial community than water samples. In all the samples, the four most dominant phyla were Proteobacteria, Cyanobacteria, Actinomycetes and Bacteroides. At the genus level, hgcI_clade and CL500-29_marine_group were the dominant bacteria shared by the water samples and sediment samples. In addition, more bacteria related to eutrophication were found in the group of BF, BC and HSB, which suggested that these ponds may have been eutrophicated. In conclusion, the present study revealed the differences in the structure and diversity of microbial communities in ponds with different aquaculture model and fish. Furthermore, changes in typical bacteria of the ponds contribute to detect water quality and prevent water eutrophication.