Permafrost-derived dissolved organic matter character controls microbial community composition in Arctic coastal waters

2021 ◽  
Author(s):  
Anders Dalhoff Bruhn ◽  
Colin A. Stedmon ◽  
Jérôme Comte ◽  
Atsushi Matsuoka ◽  
Neik Jesse Speetjens ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
The Arctic ◽  
Glacial Deposit ◽  
Deposit Type ◽  
Lacustrine Deposit

<p>Climate warming is accelerating erosion rates along permafrost-dominated Arctic coasts. To study the impact of erosion on marine microbial community composition and growth in the Arctic coastal zone, dissolved organic matter (DOM) from three representative glacial landscapes (fluvial, lacustrine and moraine) along the Yukon coastal plain, are provided as substrate to marine bacteria using a chemostat setup. Our results indicate that chemostat cultures with a flushing rate of approximately a day provide comparable DOM bioavailability estimates to those from bottle experiments lasting weeks to months. DOM composition (inferred from UV-Visible spectroscopy) and biodegradability (inferred from DOC concentration, bacterial production and respiration) significantly differed between the three glacial deposit types. DOM from fluvial and moraine deposit types shows more terrestrial characteristics with lower aromaticity (S<sub>R</sub>: 0.63 (±0.02), SUVA<sub>254</sub>: 1.65 (±0.06) respectively S<sub>R</sub>: 0.68 (±0.00), SUVA<sub>254</sub>: 1.17 (±0.06)) compared to the lacustrine deposit type (S<sub>R</sub>: 0.71 (±0.02), SUVA<sub>254</sub>: 2.15 (±0.05)). The difference in composition of DOM corresponds with the development of three distinct microbial communities, with a dominance of Alphaproteobacteria for fluvial and lacustrine deposit types (relative abundance 0.67 and 0.87 respectively) and a dominance of Gammaproteobacteria for moraine deposit type (relative abundance 0.88). Bacterial growth efficiency (BGE) is 66% for moraine-derived DOM, while 13% and 28% for fluvial-derived and lacustrine-derived DOM respectively. The three microbial communities therefore differ in their net effect on DOM utilization. The higher BGE value for moraine-derived DOM was found to be due to a larger proportion of labile colourless DOM. The results from this study, therefore indicate a substrate control of marine microbial community composition and activities, suggesting that the effect of permafrost thaw and erosion in the Arctic coastal zone will depend on subtle differences in DOM related to glacial deposit types. These differences further determines the speed and extent of DOM mineralization and thereby carbon channelling into biomass in the microbial food web. We therefore conclude that marine microbes strongly respond to the input of terrestrial DOM released during coastal erosion of Arctic glacial landscapes.</p>

scholarly journals Terrestrial Dissolved Organic Matter Mobilized From Eroding Permafrost Controls Microbial Community Composition and Growth in Arctic Coastal Zones

2021 ◽  
Vol 9 ◽  
Author(s):  
Anders Dalhoff Bruhn ◽  
Colin A. Stedmon ◽  
Jérôme Comte ◽  
Atsushi Matsuoka ◽  
Niek Jesse Speetjens ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Community Composition ◽  
Coastal Erosion ◽  
Microbial Community Composition ◽  
Marine Microbes ◽  
Glacial Deposit ◽  
Landscape Type ◽  
Deposit Type ◽  
Lacustrine Deposit

Climate warming is accelerating erosion along permafrost-dominated Arctic coasts. This results in the additional supply of organic matter (OM) and nutrients into the coastal zone. In this study we investigate the impact of coastal erosion on the marine microbial community composition and growth rates in the coastal Beaufort Sea. Dissolved organic matter (DOM) derived from three representative glacial deposit types (fluvial, lacustrine, and moraine) along the Yukon coastal plain, Canada, were used as substrate to cultivate marine bacteria using a chemostat setup. Our results show that DOM composition (inferred from UV-Visible spectroscopy) and biodegradability (inferred from DOC concentration, bacterial production and respiration) significantly differ between the three glacial deposit types. DOM derived from fluvial and moraine types show clear terrestrial characteristics with low aromaticity (Sr: 0.63 ± 0.02 and SUVA254: 1.65 ± 0.06 L mg C−1 m−1 & Sr: 0.68 ± 0.01 and SUVA254: 1.17 ± 0.06 L mg C−1 m−1, respectively) compared to the lacustrine soil type (Sr: 0.71 ± 0.02 and SUVA254: 2.15 ± 0.05 L mg C−1 m−1). The difference in composition of DOM leads to the development of three different microbial communities. Whereas Alphaproteobacteria dominate in fluvial and lacustrine deposit types (67 and 87% relative abundance, respectively), Gammaproteobacteria is the most abundant class for moraine deposit type (88% relative abundance). Bacterial growth efficiency (BGE) is 66% for DOM from moraine deposit type, while 13 and 28% for DOM from fluvial and lacustrine deposit types, respectively. The three microbial communities therefore differ strongly in their net effect on DOM utilization depending on the eroded landscape type. The high BGE value for moraine-derived DOM is probably caused by a larger proportion of labile colorless DOM. These results indicate that the substrate controls marine microbial community composition and activities in coastal waters. This suggests that biogeochemical changes in the Arctic coastal zone will depend on the DOM character of adjacent deposit types, which determine the speed and extent of DOM mineralization and thereby carbon channeling into the microbial food web. We conclude that marine microbes strongly respond to the input of terrestrial DOM released by coastal erosion and that the landscape type differently influence marine microbes.

scholarly journals Direct evidence for the role of microbial community composition in the formation of soil organic matter composition and persistence

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Luiz A. Domeignoz-Horta ◽  
Melissa Shinfuku ◽  
Pilar Junier ◽  
Simon Poirier ◽  
Eric Verrecchia ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Organic Matter ◽  
Microbial Community ◽  
Soil Organic Matter ◽  
Microbial Communities ◽  
Soil Carbon ◽  
Community Composition ◽  
Direct Evidence ◽  
Microbial Community Composition ◽  
Soil Matrix

AbstractThe largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earth’s climate warms depends in part on the persistence of soil organic carbon. Microbial turnover forms the backbone of soil organic matter (SOM) formation and it has been recently proposed that SOM molecular complexity is a key driver of stability. Despite this, the links between microbial diversity, chemical complexity and biogeochemical nature of SOM remain missing. Here we tested the hypotheses that distinct microbial communities shape the composition of SOM, and microbial-derived SOM has distinct decomposition potential depending on its community of origin. We inoculated microbial communities of varying diversities into a model soil matrix amended with simple carbon (cellobiose) and measured the thermal stability of the resultant SOM. Using a Rock-Eval® ramped thermal analysis, we found that microbial community composition drives the chemical fingerprint of soil carbon. While diversity was not a driver of SOM composition, bacteria-only communities lead to more thermally labile soil C pools than communities with bacteria and fungi. Our results provide direct evidence for a link between microbial community structure, SOM composition, and thermal stability. This evidence demonstrates the relevance of soil microorganisms in building persistent SOM stocks.

scholarly journals Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4508 ◽  
Author(s):  
Marja I. Roslund ◽  
Mira Grönroos ◽  
Anna-Lea Rantalainen ◽  
Ari Jumpponen ◽  
Martin Romantschuk ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Community Composition ◽  
Relative Abundance ◽  
Urban Soils ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Organic Matter Content ◽  
Matter Content ◽  
Molecular Weights

Background Polycyclic aromatic hydrocarbons (PAHs) accumulate in urban soils, and PAH contamination can change soil microbial community composition. Environmental microbiota is associated with human commensal microbiota, immune system and health. Therefore, studies investigating the degradation of PAHs, and the consequences of soil pollution on microbial communities in urban landscaping materials, are crucial. Methods Four landscaping materials (organic matter 1, 2, 13 and 56%) were contaminated with PAHs commonly found at urban sites (phenanthrene, fluoranthene, pyrene, chrysene and benzo(b)fluoranthene) in PAH concentrations that reflect urban soils in Finland (2.4 µg g -1 soil dry weight). PAHs were analyzed initially and after 2, 4, 8 and 12 weeks by gas chromatography-mass spectrometry. Half-lives of PAHs were determined based on 12-weeks degradation. Bacterial communities were analyzed at 1 and 12 weeks after contamination using Illumina MiSeq 16S rRNA gene metabarcoding. Results Half-lives ranged from 1.5 to 4.4 weeks for PAHs with relatively low molecular weights (phenanthrene, fluoranthene and pyrene) in landscaping materials containing 1–2% organic matter. In contrast, in materials containing 13% and 56% organic matter, the half-lives ranged from 2.5 to 52 weeks. Shorter half-lives of phenanthrene and fluoranthene were thus associated with low organic matter content. The half-life of pyrene was inversely related to the relative abundance of Beta-, Delta- and Gammaproteobacteria, and diversity of Bacteroidetes and Betaprotebacteria. Compounds with higher molecular weights followed compound-specific patterns. Benzo(b)fluoranthene was resistant to degradation and half-life of chrysene was shorter when the relative abundance of Betaproteobacteria was high. Temporal microbiota changes involved increase in the relative abundance of Deltaproteobacteria and decrease in genera Flavobacterium and Rhodanobacter. Exposure to PAHs seems to adjust microbial community composition, particularly within class Beta- and Deltaproteobacteria. Conclusions In this study, PAH degradation depended on the organic matter content and bacterial community composition of landscaping materials. Contamination seems to alter bacterial community composition in landscaping materials depending on material type. This alteration includes changes in bacterial phyla associated with human health and immune system. This may open new possibilities for managing urban environments by careful selection of landscaping materials, to benefit health and wellbeing.

scholarly journals On giant shoulders: how a seamount affects the microbial community composition of seawater and sponges

2020 ◽  
Vol 17 (13) ◽  
pp. 3471-3486 ◽  
Author(s):  
Kathrin Busch ◽  
Ulrike Hanz ◽  
Furu Mienis ◽  
Benjamin Mueller ◽  
Andre Franke ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Benthic Invertebrates ◽  
Dissolved Inorganic Carbon ◽  
Microbial Community Composition ◽  
The Arctic ◽  
Sponge Species ◽  
Rrna Gene ◽  
Sea Floor

Abstract. Seamounts represent ideal systems to study the influence and interdependency of environmental gradients at a single geographic location. These topographic features represent a prominent habitat for various forms of life, including microbiota and macrobiota, spanning benthic as well as pelagic organisms. While it is known that seamounts are globally abundant structures, it still remains unclear how and to which extent the complexity of the sea floor is intertwined with the local oceanographic mosaic, biogeochemistry, and microbiology of a seamount ecosystem. Along these lines, the present study aimed to explore whether and to what extent seamounts can have an imprint on the microbial community composition of seawater and of sessile benthic invertebrates, sponges. For our high-resolution sampling approach of microbial diversity (16S rRNA gene amplicon sequencing) along with measurements of inorganic nutrients and other biogeochemical parameters, we focused on the Schulz Bank seamount ecosystem, a sponge ground ecosystem which is located on the Arctic Mid-Ocean Ridge. Seawater samples were collected at two sampling depths (mid-water, MW, and near-bed water, BW) from a total of 19 sampling sites. With a clustering approach we defined microbial microhabitats within the pelagic realm at Schulz Bank, which were mapped onto the seamount's topography and related to various environmental parameters (such as suspended particulate matter, SPM; dissolved inorganic carbon, DIC; silicate, SiO4-; phosphate, PO43-; ammonia, NH4+; nitrate, NO32-; nitrite, NO2-; depth; and dissolved oxygen, O2). The results of our study reveal a “seamount effect” (sensu stricto) on the microbial mid-water pelagic community at least 200 m above the sea floor. Further, we observed a strong spatial heterogeneity in the pelagic microbial landscape across the seamount, with planktonic microbial communities reflecting oscillatory and circulatory water movements, as well as processes of bentho-pelagic coupling. Depth, NO32-, SiO4-, and O2 concentrations differed significantly between the determined pelagic microbial clusters close to the sea floor (BW), suggesting that these parameters were presumably linked to changes in microbial community structures. Secondly, we assessed the associated microbial community compositions of three sponge species along a depth gradient of the seamount. While sponge-associated microbial communities were found to be mainly species-specific, we also detected significant intra-specific differences between individuals, depending on the pelagic near-bed cluster they originated from. The variable microbial phyla (i.e. phyla which showed significant differences across varying depth, NO32-, SiO4-, O2 concentrations, and different from local seawater communities) were distinct for every sponge species when considering average abundances per species. Variable microbial phyla included representatives of both those taxa traditionally counted for the variable community fraction and taxa counted traditionally for the core community fraction. Microbial co-occurrence patterns for the three examined sponge species Geodia hentscheli, Lissodendoryx complicata, and Schaudinnia rosea were distinct from each other. Over all, this study shows that topographic structures such as the Schulz Bank seamount can have an imprint (seamount effect sensu lato) on both the microbial community composition of seawater and sessile benthic invertebrates such as sponges by an interplay between the geology, physical oceanography, biogeochemistry, and microbiology of seamounts.

Composition of low molecular weight organic substances affect total soil microbial activity independently of community composition.

2020 ◽  
Author(s):  
Louis J.P. Dufour ◽  
Anke. M. Herrmann ◽  
Julie Leloup ◽  
Cédric Przybylski ◽  
Luc Abbadie ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Activity ◽  
Community Composition ◽  
Metabolic Pathways ◽  
Heat Dissipation ◽  
Energy Content ◽  
Microbial Community Composition ◽  
Total Heat

<p>It has recently been suggested that microbial-derived material is an important constituent of soil organic matter, and accumulation of organic matter in soil is related to microbial activity and the composition of the microbial communities present. However, microbial activity is generally intimately related to the properties of the carbon substrate (e.g. molecular diversity, energy content) available for decomposition. It is important, therefore, to understand in more detail what the drivers of microbial activity and their associated metabolic pathways are: the composition of the microbial communities or the properties of the available organic substrate.</p><p>Water extractable organic matter from 6 different grassland and forest soils were added cross-wise to samples of each of the soils. The total heat dissipation was measured by isothermal calorimetry during a 23 h incubation period. Heat dissipation is a measure of total metabolic activity in the soil. The total CO<sub>2</sub> emission was also determined, by gas chromatography-mass spectrometry. The elemental composition of low molecular weight organic substances (LMWOS) was obtained by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry, which allowed us to calculate the Nominal Oxidation State of Carbon (NOSC) from each exact molecular mass detected. The NOSC is related to the energy content of the molecules. The microbial composition was determined by 16S rRNA gene sequencing. This experimental design allowed us to evaluate potential links between microbial community composition and their metabolic pathways when different LMWOS are undergoing decomposition.</p><p>First, we found that the total heat dissipated and CO<sub>2</sub> emitted were associated with differences in the composition of LMWOS, independent of microbial community composition in the soil. We observed that the median of the total CO<sub>2</sub> emission was positively correlated with the weighted sum of the NOSC of each detected LMWOS. These results emphasise that a supply in available substrate with lower energy density (i.e. higher NOSC) may result in an increase in decarboxylation processes. Furthermore, total heat dissipated but not CO<sub>2</sub> was positively correlated to the molecular richness of LMWOS. This indicates that substrate with a higher molecular richness include also other metabolic pathways where CO<sub>2</sub> is not a decomposition end-product. Finally, we observed three different dynamics of heat dissipation during the 23 h incubation period. These dynamics were related to the microbial communities, but were independent of the LMWOS composition. The dynamic of heat dissipation were summarised by a Q<sub>t50</sub> index, i.e. the time required to release half of the heat dissipated in 23 h. The Q<sub>t50</sub> index was significantly correlated to the relative abundance of different bacterial taxa. In conclusion, whilst the short-term dynamics of substrate use appear to be associated with microbial community composition, the overall activity is more closely related to the composition of the available substrate.</p>

scholarly journals Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott F. George ◽  
Noah Fierer ◽  
Joseph S. Levy ◽  
Byron Adams
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Vapor Flow ◽  
Arid Soils ◽  
Opposite Pattern ◽  
Dry Valley

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

Soil microbial communities in microaggregates are less affected by top-down effects of collembolans than those in macroaggregates

2021 ◽  
Author(s):  
Amandine Erktan ◽  
MD Ekramul Haque ◽  
Jérôme Cortet ◽  
Paul Henning Krogh ◽  
Stefan Scheu
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Trophic Interactions ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Trophic Levels ◽  
Soil Matrix ◽  
Fungal Abundance

<p>Trophic regulation of microbial communities is receiving growing interest in soil ecology. Most studies investigated the effect of higher trophic levels on microbial communities at the bulk soil level. However, microbes are not equally accessible to consumers. They may be hidden in small pores and thus protected from consumers, suggesting that trophic regulation may depend on the localization of microbes within the soil matrix. As microaggregates (< 250 µm) usually are more stable than macroaggregates (> 250 µm) and embedded in the latter, we posit that they will be less affected by trophic regulations than larger aggregates. We quantified the effect of four contrasting species of collembolans (Ceratophysella denticulata, Protaphorura fimata, Folsomia candida, Sinella curviseta) on the microbial community composition in macro- (250 µm – 2mm) and microaggregates (50 – 250 µm). To do so, we re-built consumer-prey systems comprising remaining microbial background (post-autoclaving), fungal prey (Chaetomium globosum), and collembolan species (added as single species or combined). After three months, we quantified microbial community composition using phospholipid fatty acid markers (PLFAs). We found that the microbial communities in macroaggregates were more affected by the addition of collembolans than the communities in microaggregates. In particular, the fungal-to-bacterial (F:B) ratio significantly decreased in soil macroaggregates in the presence of collembolans. In the microaggregates, the F:B ratio remained lower and unaffected by collembolan inoculation. Presumably, fungal hyphae were more abundant in macroaggregates because they offered more habitat space for them, and the collembolans reduced fungal abundance because they consumed them. On the contrary, microaggregates presumably contained microbial communities protected from consumers. In addition, collembolans increased the formation of macroaggregates but did not influence their stability, despite their negative effect on fungal abundance, a well-known stabilizing agent. Overall, we show that trophic interactions between microbial communities and collembolans depend on the aggregate size class considered and, in return, soil macroaggregation is affected by these trophic interactions.</p>

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

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

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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