Environmental Microbial Ecology Research Articles

Swine farm environmental microbiome: exploring microbial ecology and functionality across farms with high and low sanitary status.

Stringent regulations in pig farming, such as antibiotic control and the ban on certain additives and disinfectants, complicate disease control efforts. Despite the evolution of microbial communities inside the house environment, they maintain stability over the years, exhibiting characteristics specific to each type of production and, in some cases, unique to a particular company or farm production type. In addition, some infectious diseases are recurrent in specific farms, while other farms never present these diseases, suggesting a connection between the presence of these microorganisms in animals or their environment. Therefore, the aim of this study was to characterise environmental microbiomes of farms with high and low sanitary status, establishing the relationships between both, health status, environmental microbial ecology and its functionality. For this purpose, 6 pig farms were environmentally sampled. Farms were affiliated with a production company that handle the majority of the pigs slaughtered in Spain. This study investigated the relationship among high health and low health status farms using high throughput 16S rRNA gene sequencing. In addition, to identify ecologically relevant functions and potential pathogens based on the 16S rRNA gene sequences obtained, functional Annotation with PROkaryotic TAXa (FAPROTAX) was performed. This study reveals notable differences in microbial communities between farms with persistent health issues and those with good health outcomes, suggesting a need for protocols tailored to address specific challenges. The variation in microbial populations among farms underscores the need for specific and eco-friendly cleaning and disinfection protocols. These measures are key to enhancing the sustainability of livestock farming, ensuring safer products and boosting competitive edge in the market.

Single-Cell Techniques in Environmental Microbiology

Environmental microbiology has been an essential part of environmental research because it provides effective solutions to most pollutants. Hence, there is an interest in investigating microorganism behavior, such as observation, identification, isolation of pollutant degraders, and interactions between microbial species. To comprehensively understand cell heterogeneity, diverse approaches at the single-cell level are demanded. Thus far, the traditional bulk biological tools such as petri dishes are technically challenging for single cells, which could mask the heterogeneity. Single-cell technologies can reveal complex and rare cell populations by detecting heterogeneity among individual cells, which offers advantages of higher resolution, higher throughput, more accurate analysis, etc. Here, we overviewed several single-cell techniques on observation, isolation, and identification from aspects of methods and applications. Microscopic observation, sequencing identification, flow cytometric identification and isolation, Raman spectroscopy-based identification and isolation, and their applications are mainly discussed. Further development on multi-technique integrations at the single-cell level may highly advance the research progress of environmental microbiology, thereby giving more indication in the environmental microbial ecology.

Removing Host-derived DNA Sequences from Microbial Metagenomes via Mapping to Reference Genomes.

DNA sequencing has become a common tool in environmental microbial ecology, facilitating characterization of microbial populations as well as complex microbial communities by circumventing culture bottlenecks. However, certain samples especially from host-associated environments (rhizosphere, human tissue) or complex communities (soils) can contain a high degree of DNA sequences derived from hosts (plants, human) or other organisms of non-interest (arthropods, unicellular eukaryotes). This chapter presents a simple in silico method to remove contaminating sequences in metagenomes based on aligning sequences to reference genomes of the target organism.

Differences in microbiome and virome between cattle and horses in the same farm.

ObjectiveThe ecosystem of an animal farm is composed of various elements, such as animals, farmers, plants, feed, soil, and microorganisms. A domesticated animal’s health is largely connected with the reservoir of bacteria and viruses in animal farms. Although a few studies have focused on exploring the gut microbiome of animals, communities of microbiota and viruses in feedlots have not been thoroughly investigated.MethodsHere, we collected feces and dust samples (4 groups: cattle feces, C_F; horse feces, H_F; cattle dust, C_D; and horse dust, H_D) from cattle and horse farms sharing the same housing and investigated their microbiome/virome communities by Illumina sequencing.ResultsDust groups (C_D and H_D) showed higher microbial diversity than feces groups (C_F and H_F) regardless of animal species. From the microbial community analysis, all the samples from the four groups have major phyla such as Proteobacteria (min 37.1% to max 42.8%), Firmicutes (19.1% to 24.9%), Bacteroidetes (10.6% to 22.1%), and Actinobacteria (6.1% to 20.5%). The abundance of Streptococcus, which commonly recognized as equine pathogens, was significantly higher in the horse group (H_D and H_F). Over 99% among the classified virome reads were classified as Caudovirales, a group of tailed bacteriophages, in all four groups. Foot-and-mouth disease virus and equine adenovirus, which cause deadly diseases in cattle and horse, respectively, were not detected.ConclusionOur results will provide baseline information to understand different gut and environmental microbial ecology between two livestock species.

Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation

Light-flavour Baijiu is a type of Chinese liquor with a pure and mild flavour produced by traditional spontaneous solid-state fermentation. The flavour of this liquor has been found to vary in the different periods of annual production. To explore the factors affecting flavour, the microbiota of the surrounding environment, starter and fermentation process in different periods were investigated. Results showed that the ester content and acidity of light-flavour Baijiu were significantly lower when annual production was resumed after a summer break. HCA plot of volatile flavour profile and bacterial PCoA results indicated that the differences occurred at later stages, mainly due to different structures of Lactobacillus. Correlation analysis by O2PLS indicated that Lactobacillus positively correlated with esters. Species-level analysis showed that the lack of L. acetotolerans on the surface of the jar might cause a lag in fermentation and lower ester content. Thereafter, L. acetotolerans was revived during fermentation and enriched on the surface of the jar, which promoted ester formation. As important sources of L. acetotolerans, the air and fermentation jars played a critical role during fermentation. Therefore, this systematic study on environmental microbial ecology is valuable for quality control and to explore environmental microbiota functions during spontaneous fermentation.

Revisiting life strategy concepts in environmental microbial ecology

Microorganisms are physiologically diverse, possessing disparate genomic features and mechanisms for adaptation (functional traits), which reflect on their associated life strategies and determine at least to some extent their prevalence and distribution in the environment. Unlike animals and plants, there is an unprecedented diversity and intractable metabolic versatility among bacteria, making classification or grouping these microorganisms based on their functional traits as has been done in animal and plant ecology challenging. Nevertheless, based on representative pure cultures, microbial traits distinguishing different life strategies had been proposed, and had been the focus of previous reviews. In the environment, however, the vast majority of naturally occurring microorganisms have yet to be isolated, restricting the association of life strategies to broad phylogenetic groups and/or physiological characteristics. Here, we reviewed the literature to determine how microbial life strategy concepts (i.e. copio- and oligotrophic strategists, and competitor-stress tolerator-ruderals framework) are applied in complex microbial communities. Because of the scarcity of direct empirical evidence elucidating the associated life strategies in complex communities, we rely heavily on observational studies determining the response of microorganisms to (a)biotic cues (e.g. resource availability) to infer microbial life strategies. Although our focus is on the life strategies of bacteria, parallels were drawn from the fungal community. Our literature search showed inconsistency in the community response of proposed copiotrophic- and oligotrophic-associated microorganisms (phyla level) to changing environmental conditions. This suggests that tracking microorganisms at finer phylogenetic and taxonomic resolution (e.g. family level or lower) may be more effective to capture changes in community response and/or that edaphic factors exert a stronger effect in community response. We discuss the limitations and provide recommendations for future research applying microbial life strategies in environmental studies.

Comparison of three clustering approaches for detecting novel environmental microbial diversity.

Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR2) database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR2. Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity.

Drying–Rewetting Cycles Affect Fungal and Bacterial Growth Differently in an Arable Soil

Drying and rewetting is a frequent physiological stress for soil microbial communities; a stress that is predicted to grow more influential with future climate change. We investigated the effect of repeated drying-rewetting cycles on bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth, on the biomass concentration and composition (PLFA), and on the soil respiration. Using different plant material amendments, we generated soils with different initial fungal:bacterial compositions that we exposed to 6-10 repetitions of a drying-rewetting cycle. Drying-rewetting decreased bacterial growth while fungal growth remained unaffected, resulting in an elevated fungal:bacterial growth ratio. This effect was found irrespective of the initial fungal:bacterial biomass ratio. Many drying-rewetting cycles did not, however, affect the fungal:bacterial growth ratio compared to few cycles. The biomass response of the microbial community differed from the growth response, with fungal and total biomass only being slightly negatively affected by the repeated drying-rewetting. The discrepancy between growth- and biomass-based assessments underscores that microbial responses to perturbations might previously have been misrepresented with biomass-based assessments. In light of this, many aspects of environmental microbial ecology may need to be revisited with attention to what measure of the microbial community is relevant to study.

The Plate Debate: Cultivable communities have no utility in contemporary environmental microbial ecology

Contention: ‘Community-scale characterizations based on cultivable microbes are so unrepresentative that they have no utility in contemporary environmental microbial ecology’ . Microbes are, by definition, very small. Individual microbial cells and isolated fungal hyphae are invisible to the unaided human eye, and remained intangible until the invention of microscopes in the 17th Century. Aggregations of microbial cells to form larger-scale and visible entities occur naturally and can be spectacularly manifest, for example as bacterial slimes, myxomycete plasmodia, and fungal basidiocarps. In the history of microbiology, there was an imperative not just simply to visualize microbial cells, but to enumerate them and understand their form, physiology, function and relationships with their environment. This required the isolation, purification and multiplication of cells to provide sufficient biomass to enable analyses. This was conveniently achieved using dispersal and dilution techniques, most commonly in an aqueous medium, followed by modest enrichment on semisolid media, such that ostensibly separated cells proliferated and formed visible colonies; enumeration was then based on these so-called CFUs, in recognition of the fact that it was not necessarily a single cell that was the originator. Such techniques were pioneered by Koch in the 1880s, who first used cut surfaces of boiled potatoes as an enrichment surface, and then adopted hydrated gelatine films, which were better suited to visualization of colonies. Methods then evolved which adopted other gelling agents, most notably agar, and a huge variety of nutritional supplements to such media as it became apparent that different organisms grew more or less effectively on a variety of substrates. Media were devised that were apparently selective to restricted groups or even species of microbe. These techniques revolutionized both medical and environmental microbiology. In a medical context, the ability to isolate disease-causing microorganisms in a selective manner enabled Koch to formulate and apply …

Cultivation gives context to the microbial ecologist

The posed debate asks whether cultivation has a place in contemporary environmental microbial ecology. Approximately two decades ago, cultivation-independent methods experienced an advance (Olsen et al. , 1986) concurrent with the establishment in the literature of the following sentence: ‘It is well known that 99.9% of all organisms are unculturable’ (Rothschild, 2006). While technical advancements have been made in sequence-based and cultivation-based microbial ecology, the ‘uncultivability’ of environmental microorganisms has stood as a beacon to the molecular community of the futility of cultivation. The same phenomenon has served as a welcome challenge to others, leading to the development of novel cultivation approaches and technologies. It appears now that microbial cultivation is an emerging frontier in environmental microbiology, in part because it provides information about communities that cannot be obtained directly from sequencing efforts alone (Ellis et al. , 2003). As the barriers to cultivation are reduced, the complications of undertaking microbial ecology in its absence are becoming more apparent. Sequence collection efforts may appear, at first glance, far superior to cultivation because they bypass the discrepancy between the number of microbial cells present in a sample and the number of colonies produced in vitro (Schloss & Handelsman, 2005). The promise of genomes without cultivation has made metagenomics a popular cultivation-independent approach to microbial community assessment (Handelsman, 2004; DeLong, 2005). Isolation and sequencing of microbial DNA from mixed communities en masse, rather than focusing on select phylogenetic markers, potentially provides access to the full complement of microbial genes and the opportunity to reassemble genomes without the requirement of environmental isolates (Handelsman et al. , 1998). However, closing genomes from these efforts proves exceedingly difficult, apparently owing to genomic micro-heterogeneity (Tringe & Rubin, 2005), compounded by species diversity within samples (Venter et al. , 2004). Even with closure, typically 40% or …

Environmental Microbial Ecology in an “Omics” Era

Environmental Microbial Ecology in an “Omics” Era