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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.

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.

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.

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.