Microbial Responses To Environmental Changes

Advances in next generation sequencing technologies, omics, and bioinformatics are revealing a tremendous and unsuspected diversity of microbes, both at a compositional and functional level. Moreover, the expansion of ecological concepts into microbial ecology has greatly advanced our comprehension of the role microbes play in the functioning of ecosystems across a wide range of biomes. Super-imposed on this new information about microbes, their functions and how they are organized, environmental gradients are changing rapidly, largely driven by direct and indirect human activities. In the context of global change, understanding the mechanisms that shape microbial communities is pivotal to predict microbial responses to novel selective forces and their implications at the local as well as global scale. One of the main features of microbial communities is their ability to react to changes in the environment. Thus, many studies have reported changes in the performance and composition of communities along environmental gradients. However, the mechanisms underlying these responses remain unclear. It is assumed that the response of microbes to changes in the environment is mediated by a complex combination of shifts in the physiological properties, single-cell activities, or composition of communities: it may occur by means of physiological adjustments of the taxa present in a community or selecting towards more tolerant/better adapted phylotypes. Knowing whether certain factors trigger one, many, or all mechanisms would greatly increase confidence in predictions of future microbial composition and processes. This Research Topic brings together studies that applied the latest molecular techniques for studying microbial composition and functioning and integrated ecological, biogeochemical and/or modeling approaches to provide a comprehensive and mechanistic perspective of the responses of micro-organisms to environmental changes. This Research Topic presents new findings on environmental parameters influencing microbial communities, the type and magnitude of response and differences in the response among microbial groups, and which collectively deepen our current understanding and knowledge of the underlying mechanisms of microbial structural and functional responses to environmental changes and gradients in both aquatic and terrestrial ecosystems. The body of work has, furthermore, identified many challenges and questions that yet remain to be addressed and new perspectives to follow up on.

Microbial community composition and functional potential can be affected by human-derived environmental changes during the Anthropocene with important consequences for elemental cycling and whole ecosystem processes. This study tested the hypothesis that environmental changes impact microbial communities across different spatial and temporal scales. The main objectives of this study were to determine 1) biocorrosion-causing organism colonization and abundance on man-made steel structures, 2) the identity and function of a core microbiome across steel microbial communities, and 3) the response of coastal microbial communities to extreme hurricane disturbance events. Steel microbiomes represent microbial responses to environmental disturbance (i.e., introduction of a novel substrate and surface environment) on small spatial scales but long temporal scales. Conversely, microbial responses to extreme storm events provide insight into disturbances affecting large spatial scales but short temporal scales. Stainless steel (304 and 316) deployments along salinity gradients in two North Carolina estuarine river systems resulted in increased colonization of iron-oxidizing bacteria on more-corrosion-resistant stainless steel (316) and at higher salinities. A novel iron-oxidizer species Mariprofundus erugo was isolated and sequenced, revealing genes for molybdenum utilization and reactive oxygen species protection, which may represent adaptations towards advanced steel types. Comparisons of microbial communities across stainless steel and historic ferrous-hulled shipwreck steel in the Pamlico Sound, NC revealed a "core steel microbiome" of heterotrophic generalists that likely play important roles in biofilm protection and functional stability for biocorrosion communities. Shifting scales, extreme hurricane events were correlated with changes in total (DNA) and active (RNA) coastal bacterial but not archaeal communities, and in the water column but not in sediments. Offshore marine sites exhibited decreased community diversity and evenness and increased abundance of copiotrophs. Hurricanes were also correlated with increased putative function of pathogenic taxa (i.e., Prevotella and Legionella) and lignin-degrading taxa, likely causing decreased water quality and increased bacterial production. These environmental disturbances across different spatial and temporal scales show that microbial communities are constantly responding and adapting to survive. Microbial communities have shown to be extremely resilient to Anthropocene conditions, and the microbial responses in this study can be applied to better understand future global change scenarios.

Microbiome Under Changing Climate: Implications and Solutions presents the latest biotechnological interventions for the judicious use of microbes to ensure optimal agricultural yield. Summarizing aspects of vulnerability, adaptation and amelioration of climate impact, this book provides an important resource for understanding microbes, plants and soil in pursuit of sustainable agriculture and improved food security. It emphasizes the interaction between climate and soil microbes and their potential role in promoting advanced sustainable agricultural solutions, focusing on current research designed to use beneficial microbes such as plant growth promoting microorganisms, fungi, endophytic microbes, and more. Changes in climatic conditions influence all factors of the agricultural ecosystem, including adversely impacting yield both in terms of quantity and nutritional quality. In order to develop resilience against climatic changes, it is increasingly important to understand the effect on the native micro-flora, including the distribution of methanogens and methanotrophs, nutrient content and microbial biomass, among others. Demonstrates the impact of climate change on secondary metabolites of plants and potential responses Incorporates insights on microflora of inhabitant soil Explores mitigation processes and their modulation by sustainable methods Highlights the role of microbial technologies in agricultural sustainability

The Arctic is undergoing a rapid environmental shift with increasing temperatures and precipitations expected to continue over the next century. Yet, little is known about how microbial communities and their underlying metabolic processes will respond to ongoing climatic changes. To address this question, we focused on Lake Hazen, NU, Canada. As the largest High Arctic lake by volume, it is a unique site to investigate microbial responses to environmental changes. Over the past decade, glacial coverage of the lake has declined. Increasing glacial runoff and sedimentation rates in the lake has resulted in differential influx of nutrients through spatial gradients. I used these spatial gradients to study how environmental changes might affect microbial community structure and functional capacity in Arctic lakes. I performed a metagenomic analysis of microbial communities from hydrological regimes representing high, low, and negligible influence of glacial runoff and compared the observed structure and function to the natural geochemical gradients. Genes and reconstructed genomes found in different abundances across these sites suggest that high-runoff regimes alter geochemical gradients, homogenise the microbial structure, and reduce genetic diversity. This work shows how a genome-centric metagenomics approach can be used to predict future microbial responses to a changing climate.

The cryosphere stands for environments where water appears in a frozen form. It includes permafrost, glaciers, ice sheets, and sea ice and is currently more affected by Global Change than most other regions of the Earth. In the cryosphere, limited water availability and subzero temperatures cause extreme conditions for all kind of life which microorganisms can cope with extremely well. The cryosphere’s microbiota displays an unexpectedly large genetic potential, and taxonomic as well as functional diversity which, however, we still only begin to map. Also, microbial communities influence reaction patterns of the cryosphere towards Global Change. Altered patterns of seasonal temperature fluctuations and precipitation are expected in the Arctic and will affect the microbial turnover of soil organic matter (SOM). Activation of nutrients by thawing and increased active layer thickness as well as erosion renders nutrient stocks accessible to microbial activities. Also, glacier melt and retreat stimulate microbial life in turn influencing albedo and surface temperatures. In this context, the functional resilience of microbial communities in the cryosphere is of major interest. Particularly important is the ability of microorganisms and microbial communities to respond to changes in their surroundings by intracellular regulation and population shifts within functional niches, respectively. Research on microbial life exposed to permanent freeze or seasonal freeze-thaw cycles has led to astonishing findings about microbial versatility, adaptation, and diversity. Microorganisms thrive in cold habitats and new sequencing techniques have produced large amounts of genomic, metagenomic, and metatranscriptomic data that allow insights into the fascinating microbial ecology and physiology at low and subzero temperatures. Moreover, some of the frozen ecosystems such as permafrost constitute major global carbon and nitrogen storages, but can also act as sources of the greenhouse gases methane and nitrous oxide. In this book we summarize state of the art knowledge on whether environmental changes are met by a flexible microbial community retaining its function, or if the altered conditions also render the community in a state of altered properties that affect the Earth’s element cycles and climate. This book brings together research on the cryosphere’s microbiota including permafrost, glaciers, and sea ice in Arctic and Antarctic regions. Different spatial scales and levels of complexity are considered, spanning from ecosystem level to pure culture studies of model microbes in the laboratory. It aims to attract a wide range of parties with interest in the effect of climate change and/or low temperatures on microbial nutrient cycling and physiology.

Marine environments are fluid. Microorganisms living in the ocean experience diverse environmental changes over wide spatiotemporal scales. For microorganisms and their communities to survive and function in the ocean, they need to have the capacity to sense, respond to, adapt to and/or withstand periodic and sporadic environmental changes. This eBook collates a variety of recent research reports and theoretical discussions on the ecoenergetic strategies, community structure, biogeochemical and ecosystem functions as well as regulatory processes and mechanisms that marine microorganisms employ in response to environmental gradients and variations.

The ongoing global climate change triggered by greenhouse gas growth has had a significant effect on the microbial dynamics of plants and soils. This volume explores the various microbial responses of plants and soils caused directly or indirectly by climate change resulting from rising greenhouse gases and other factors. The book considers the rapidly changing environment and the important role of microbiomes in restoring soil and plant health and in creating sustainable approaches. It discusses the adaptation and mitigation of plants and soils, specifically addressing such topics as biogeochemical processes, antimicrobial resistance, the dynamics of bacteria and fungus in extreme environments, bacterial siderophores for sustainability, and more. The volume also looks at edaphic and regeneration performance of tree species in the temperate forests.

People's desire to understand the environments in which they live is a natural one. People spend most of their time in spaces and structures designed, built, and managed by humans, and it is estimated that people in developed countries now spend 90 percent of their lives indoors. As people move from homes to workplaces, traveling in cars and on transit systems, microorganisms are continually with and around them. The human-associated microbes that are shed, along with the human behaviors that affect their transport and removal, make significant contributions to the diversity of the indoor microbiome. The characteristics of "healthy" indoor environments cannot yet be defined, nor do microbial, clinical, and building researchers yet understand how to modify features of indoor environmentsâ€"such as building ventilation systems and the chemistry of building materialsâ€"in ways that would have predictable impacts on microbial communities to promote health and prevent disease. The factors that affect the environments within buildings, the ways in which building characteristics influence the composition and function of indoor microbial communities, and the ways in which these microbial communities relate to human health and well-being are extraordinarily complex and can be explored only as a dynamic, interconnected ecosystem by engaging the fields of microbial biology and ecology, chemistry, building science, and human physiology. This report reviews what is known about the intersection of these disciplines, and how new tools may facilitate advances in understanding the ecosystem of built environments, indoor microbiomes, and effects on human health and well-being. It offers a research agenda to generate the information needed so that stakeholders with an interest in understanding the impacts of built environments will be able to make more informed decisions.

The book provides an overview relevant to various biological mechanisms that regulate carbon exchanges between the major components and their response to climate change. Climate change has a significant impact on people's lives, energy demand, food security, etc. The soil microbial ecology is vital for assessing terrestrial and aquatic carbon cycles and climate feedback. However, the primary concern is the complexity of the soil microbial community and its severely affected functions due to the climate and other global changes. Global warming comprises an assessment of the dynamic interactions and feedback between microbes, plants, and their physical environment due to climate change. The book will address the need to use a multifactor experimental approach to understand how soil microorganisms and their activities adapt to climate change and the implications of carbon cycle feedback. The most pressing concern is a clearer understanding of the biological factors that regulate carbon exchanges between land, oceans, and the atmosphere and how these exchanges will respond to climate change via climate–ecosystem feedbacks, which could augment or quell regional and global climate change. Terrestrial ecosystems play an important role in climate feedback as they produce and absorb greenhouse gases like carbon dioxide, methane, and nitrous oxides. They also strongly contribute to storing enormous amounts of carbon in living vegetation and soils, rendering them a significant global carbon sink. If climate change projections are realistic, such a rapid increase in carbon loss from soil could exacerbate the soil carbon cycle feedback. The book will determine the role of microbial feedback in regulating soil-land-atmosphere carbon exchange under changing climatic conditions at the regional and global levels. The current book will also focus on recent research designed to use beneficial microbes such as plant growth-promoting microorganisms, fungi, endophytic microbes, and others to improve understanding of the interaction and their potential role in promoting advanced management for sustainable agricultural solutions. Understanding the influence on the native microbiome, such as the distribution of methanogens and methanotrophs, nutritional content, microbial biomass, and other factors, is becoming increasingly crucial to establishing climate-resilient agriculture.