Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions

ABSTRACT Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context—propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)—is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering. IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).

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Principles for engineering microbial composition and ecosystem functioning

10.1101/730556 ◽

2019 ◽

Cited By ~ 1

Author(s):

Michaeline B.N. Albright ◽

Sanna Sevanto ◽

La Verne Gallegos-Graves ◽

John Dunbar

Keyword(s):

Microbial Community ◽

Community Composition ◽

Ecosystem Functioning ◽

Functional Outcomes ◽

Propagule Pressure ◽

Biotic Interactions ◽

Plant Litter ◽

Relative Importance ◽

Microbial Composition ◽

The Impact

AbstractMicrobial probiotics are designed to improve functions in diverse ecosystems, yet probiotics often fail to have the desired beneficial effects. The introduction of probiotics to an environment with a preexisting microbiome is analogous to an invasion event, but is rarely considered in this light. Here, we tested the relative importance of propagule pressure (inoculation dose and frequency) compared to biotic interactions (composition of introduced and resident communities) in driving microbial composition and functional outcomes following microbial community invasions in experimental microcosms. Ecosystem functioning was assessed through measurements of CO2 production and DOC (dissolved organic carbon) accumulation, an activity and an environmental modification metric, respectively. Further, to test the dependence of propagule pressures versus biotic interactions was dependent on environmental context, experiments were performed on two different substrates, R2A agar and plant litter. In both environments, we found that biotic interactions were more important than propagule pressure in driving microbial composition. Moreover, bacteria were more successful invaders than fungi. While successful invasion is a first step, ultimately the success of microbial invasions in microbiome engineering applications is measured by the impact on ecosystem functioning. As with shaping the microbiome composition, biotic interactions were key to functional outcomes, but the magnitude of the functional impact varied by environment. Identifying general principles that determine the community composition and functioning following microbial invasions is key to efficient community engineering.SignificanceWith increasing frequency humans are introducing new microbes into pre-existing microbiomes to alter functioning. Examples include, modification of microflora in human guts for better health, and soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved by better understanding of microbial invasions. We conducted a microbial community invasion experiment, to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).

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PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

Journal of Animal Science ◽

10.1093/jas/skz258.594 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 293-294

Author(s):

Camila S Marcolla ◽

Benjamin Willing

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Relative Abundance ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Poultry Production ◽

Microbiota Composition ◽

Microbial Composition ◽

The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

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The impact of immigration on microbial community composition in full-scale anaerobic digesters

Scientific Reports ◽

10.1038/s41598-017-09303-0 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 53

Author(s):

Rasmus H. Kirkegaard ◽

Simon J. McIlroy ◽

Jannie M. Kristensen ◽

Marta Nierychlo ◽

Søren M. Karst ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Microbial Community Composition ◽

Full Scale ◽

Anaerobic Digesters ◽

The Impact

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Impacts of near‑future ocean warming on microbial community composition of the stomach of the soft‑bottom sea star Luidia clathrata (Say) (Echinodermata: Asteroidea)

10.21203/rs.3.rs-306104/v1 ◽

2021 ◽

Author(s):

Michelle D Curtis ◽

Casey D Morrow ◽

James B McClintock

Keyword(s):

Microbial Community ◽

Community Composition ◽

Seawater Temperature ◽

Microbial Community Composition ◽

Experimental Temperature ◽

Sea Star ◽

Soft Bottom ◽

Cardiac Stomach ◽

Luidia Clathrata ◽

The Impact

Abstract There is growing evidence that environmental changes caused by climate change can impact the microbiome of marine invertebrates. Such changes can have important implications for the overall health of the host. In the present study we investigated the impact of chronic exposure to an ambient (28°C) and a predicted mid- (30°C) and end-of-century (32°C) seawater temperature on microbiome modification in tissues of the cardiac stomach of the abundant predatory sea star Luidia clathrata collected in September 2018 from Apalachee Bay, Florida (29°58’N, 84°19’W) in the northern Gulf of Mexico (GOM). Diversity (Shannon index) was lowest among the microbial community of stomach tissue when compared to the microbiome of the artificial sea star feed, and aquarium sand and seawater across all three experimental temperature treatments. Moreover, the stomach microbial community composition was distinct between each of the four sample types. Exposure to the highest experimental temperature treatment (32°C) resulted in a significant modification of the composition of the microbial community in stomach and sand samples, but not in seawater samples when compared to those from the current mean ambient GOM temperature (28°C). Importantly, at the most elevated temperature the stomach microbiome shifted from a Vibrio sp. dominated community to a more diverse community with higher proportions of additional taxa including Delftia sp. and Pseudomonas sp. This microbiome shift could impact the digestive functionality and ultimately the health of L. clathrata, a key soft-bottom predator in the northern GOM.

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Community composition and development of the post-weaning piglet gut microbiome

10.21203/rs.3.rs-60981/v1 ◽

2020 ◽

Author(s):

Daniela Gaio ◽

Matthew Z DeMaere ◽

Kay Anantanawat ◽

Graeme J Eamens ◽

Michael Liu ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Antibiotic Treatment ◽

Gut Microbiome ◽

Treatment Effects ◽

Sequence Data ◽

Microbial Community Composition ◽

Dominant Factor ◽

Microbial Composition

Abstract BackgroundEarly weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. Studies have previously investigated the effects of probiotics as alternatives to antibiotic treatment for the prevention of post-weaning diarrhea. In order to describe the post-weaning gut microbiota, and the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we processed over 800 faecal time-series samples from 126 piglets and 42 sows, generating over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial procedures, the generation of our metagenomic dataset and the analysis of the microbial community composition using a phylogenetic framework.ResultsFactors such as age, litter effects, and breed, by significantly correlating with gut microbial community shifts, can be major confounding factors in the assessment of treatment effects. Intramuscular antibiotic treatment and probiotic treatments were found to correlate with alpha and beta diversity, as well as with a transient establishment of Mollicutes and Lactobacillales, respectively. We found the abundance of certain taxa to correlate with weight gain.ConclusionsOur findings demonstrate that breed, litter, and age, are important contributors to variation in the community composition, and that treatment effects of the antibiotic and probiotic treatments were subtle, while host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The current study shows, by means of a phylogenetic diversity framework, that the post-weaning pig gut microbiome appears to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life.

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Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

Diversity ◽

10.3390/d13110525 ◽

2021 ◽

Vol 13 (11) ◽

pp. 525

Author(s):

Brianna L. Boss ◽

Bianca R. Charbonneau ◽

Javier A. Izquierdo

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Environmental Gradients ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Spatial Diversity ◽

Microbial Composition

The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

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THE IMPACT OF AGRICULTURE ON SOIL MICROBIAL COMMUNITY COMPOSITION AND DIVERSITY IN SOUTHEAST ASIA

Microbes for Climate Resilient Agriculture ◽

10.1002/9781119276050.ch2 ◽

2017 ◽

pp. 25-40

Author(s):

Binu M. Tripathi ◽

Itumeleng Moroenyane ◽

Jonathan M. Adams

Keyword(s):

Microbial Community ◽

Southeast Asia ◽

Community Composition ◽

Soil Microbial Community ◽

Microbial Community Composition ◽

Soil Microbial ◽

The Impact ◽

Soil Microbial Community Composition

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Temporal Analysis of the Microbial Community from the Crystallizer Ponds in Cabo Rojo, Puerto Rico, Using Metagenomics

Genes ◽

10.3390/genes10060422 ◽

2019 ◽

Vol 10 (6) ◽

pp. 422 ◽

Cited By ~ 5

Author(s):

Ricardo L. Couto-Rodríguez ◽

Rafael Montalvo-Rodríguez

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Community Composition ◽

Ammonia Oxidation ◽

Microbial Community Composition ◽

Temporal Analysis ◽

Hypersaline Environment ◽

Hypersaline Environments ◽

Metabolic Processes ◽

Microbial Composition

The Cabo Rojo solar salterns are a hypersaline environment located in a tropical climate, where conditions remain stable throughout the year. These conditions can favor the establishment of steady microbial communities. Little is known about the microbial composition that thrives in hypersaline environments in the tropics. The main goal of this study was to assess the microbial diversity present in the crystallizer ponds of Cabo Rojo, in terms of structure and metabolic processes across time using metagenomic techniques. Three samplings (December 2014, March and July 2016) were carried out, where water samples (50 L each) were filtered through a Millipore pressurized filtering system. DNA was subsequently extracted using physical–chemical methods and sequenced using paired end Illumina technologies. The sequencing effort produced three paired end libraries with a total of 111,816,040 reads, that were subsequently assembled into three metagenomes. Out of the phyla detected, the microbial diversity was dominated in all three samples by Euryarchaeota, followed by Bacteroidetes and Proteobacteria. However, sample MFF1 (for Muestreo Final Fraternidad) exhibited a higher diversity, with 12 prokaryotic phyla detected at 34% NaCl (w/v), when compared to samples MFF2 and MFF3, which only exhibited three phyla. Precipitation events might be one of the contributing factors to the change in the microbial community composition through time. Diversity at genus level revealed a more stable community structure, with an overwhelming dominance of the square archaeon Haloquadratum in the three metagenomes. Furthermore, functional annotation was carried out in order to detect genes related to metabolic processes, such as carbon, nitrogen, and sulfur cycles. The presence of gene sequences related to nitrogen fixation, ammonia oxidation, sulfate reduction, sulfur oxidation, and phosphate solubilization were detected. Through binning methods, four putative novel genomes were obtained, including a possible novel genus belonging to the Bacteroidetes and possible new species for the genera Natronomonas, Halomicrobium, and Haloquadratum. Using a metagenomic approach, a 3-year study has been performed in a Caribbean hypersaline environment. When compared to other salterns around the world, the Cabo Rojo salterns harbor a similar community composition, which is stable through time. Moreover, an analysis of gene composition highlights the importance of the microbial community in the biogeochemical cycles at hypersaline environments.

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