Altered protozoan and bacterial communities and survival of Escherichia coli O157:H7 in monensin-treated wastewater from a dairy lagoon

Ruminal Bacterial Community Successions in Response to Monensin Supplementation in Goats

Simple Summary

Monensin has been successfully used in the ruminants’ diets to manipulate ruminal fermentation and improve feed efficiency, but its use is facing decreased levels of social acceptance due to the potential impacts on public health. Understanding the ruminal bacterial community successions in response to monensin supplementation would help the search for alternatives. We found that the ruminal ecosystem was reshaped through a series of succession processes during the adaption to monensin rather than following a clear dichotomy between Gram-positive and Gram-negative cell types, and the carbohydrate-degrading bacteria presented a higher adaptability. Therefore, a potential alternative for monensin as a rumen modifier could be one with similar patterns of ruminal microbial community successions.

Abstract

Previous studies have demonstrated that the effects of monensin on methanogenesis and ruminal fermentation in ruminants were time-dependent. To elucidate the underlying mechanism, we investigated the ruminal bacterial community successions during the adaptation to monensin supplementation and subsequent withdrawal in goats. The experiment included a baseline period of 20 days followed by a treatment period of 55 days with 32 mg monensin/d and a washout period of 15 days. Monensin supplementation reduced the α diversity and changed the structure of ruminal microflora. The α diversity was gradually restored during adaption, but the structure was still reshaped. The temporal dynamics of 261 treatment- and/or time-associated ruminal bacteria displayed six patterns, with two as monensin-sensitive and four as monensin-resistant. The monensin sensitivity and resistance of microbes do not follow a clear dichotomy between Gram-positive and Gram-negative cell types. Moreover, the temporal dynamic patterns of different bacterial species within the same genus or family also displayed variation. Of note, the relative abundance of the total ruminal cellulolytic bacteria gradually increased following monensin treatment, and that of the total amylolytic bacteria were increased by monensin, independent of the duration. In conclusion, under the pressure of monensin, the ruminal ecosystem was reshaped through a series of succession processes, and the carbohydrate-degrading bacteria presented a higher level of adaptability.

Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community

The composition of an ecosystem is thought to be important for determining its resistance to invasion. Studies of natural ecosystems, from plant to microbial communities, have found that more diverse communities are more resistant to invasion. In some cases, more diverse communities resist invasion by more completely consuming the resources necessary for the invader. We show that Escherichia coli can successfully invade cultures of the alga Chlamydomonas reinhardtii (phototroph) or the ciliate Tetrahymena thermophila (predator) but cannot invade a community where both are present. The invasion resistance of the algae-ciliate community arises from a higher-order interaction between species (interaction modification) that is unrelated to resource consumption. We show that the mode of this interaction is the algal inhibition of bacterial aggregation, which leaves bacteria vulnerable to predation. This mode requires both the algae and the ciliate to be present and provides an example of invasion resistance through an interaction modification.

Dynamics of methanogenesis, ruminal fermentation, and alfalfa degradation during adaptation to monensin supplementation in goats

This study aimed to examine the temporal (hourly within a day and daily over the long term) effects of monensin on CH₄ emissions, ruminal fermentation, and in situ alfalfa degradation in dairy goats during dietary monensin supplementation by controlling the confounding effects of feed intake and ambient temperature. Six ruminally cannulated dairy goats were used, and they were housed in environmental chambers and fed a restricted amount of ration throughout the experiment. The experiment included a baseline period of 20 d followed by a treatment period of 55 d with 32 mg of monensin/d. During the whole experiment, CH₄ production was measured every 5 d, whereas fermentation characteristics and in situ alfalfa degradation were analyzed every 10 d. The CH₄-depressing effect of monensin was time dependent on the duration of treatment, highly effective at d 5 but thereafter decreased gradually until d 55 even though CH₄-suppressing effect still remained significant. The decreasing effects of monensin on ruminal acetate proportion and acetate to propionate ratio also faded over days of treatment, and the acetate proportion returned up to the pre-supplementation level on d 50. Monensin supplementation elevated ruminal propionate proportion and decreased the effective ruminal degradability of alfalfa NDF, but both measurements tended to recover over time. The postprandial increase rate of hourly CH₄ emissions was reduced, whereas that of propionate proportion was enhanced by monensin supplementation. However, the postprandial responses to monensin in CH₄ emission rates, ruminal VFA profiles, and in situ degradation kinetics declined with both hours after feeding and days of treatment. Our results suggest that the CH₄-suppressing effect of monensin supplementation in goats was attributed to reductions in both ruminal feed degradation and acetate to propionate ratio, but those reductions faded with time, hours after feeding, and days of treatment.

Spatial disease dynamics of free-living pathogens under pathogen predation

The epidemiological dynamics of potentially free-living pathogens are often studied with respect to a specific pathogen species (e.g., cholera) and most studies concentrate only on host-pathogen interactions. Here we show that metacommunity-level interactions can alter conventional spatial disease dynamics. We introduce a pathogen eating consumer species and investigate a deterministic epidemiological model of two habitat patches, where both patches can be occupied by hosts, pathogens, and consumers of free-living pathogens. An isolated habitat patch shows periodic disease outbreaks in the host population, arising from cyclic consumer-pathogen dynamics. On the other hand, consumer dispersal between the patches generate asymmetric disease prevalence, such that the host population in one patch stays disease-free, while disease outbreaks occur in the other patch. Such asymmetry can also arise with host dispersal, where infected hosts carry pathogens to the other patch. This indirect movement of pathogens causes also a counter-intuitive effect: decreasing morbidity in a focal patch under increasing pathogen immigration. Our results underline that community-level interactions influence disease dynamics and consistent spatial asymmetry can arise also in spatially homogeneous systems.

Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists

A wide diversity of organisms utilize faecal habitats as a rich nutrient source or a mechanism to traverse through animal hosts. We sequenced the 18S rRNA genes of the coprophilic, fruiting body-forming amoeba Guttulinopsis vulgaris and its non-fruiting relatives Rosculus 'ithacus' CCAP 1571/3, R. terrestris n. sp. and R. elongata n. sp. and demonstrate that they are related to the coprophilic flagellate Helkesimastix in a strongly supported, but highly divergent 18S sister clade. PCR primers specific to both clades were used to generate 18S amplicons from a range of environmental and faecal DNA samples. Phylogenetic analysis of the cloned sequences demonstrated a high diversity of uncharacterised sequence types within this clade, likely representing previously described members of the genera Guttulinopsis, Rosculus and Helkesimastix, as well as so-far unobserved organisms. Further, an Illumina MiSeq sequenced set of 18S V4-region amplicons generated from faecal DNAs using universal eukaryote primers showed that core-cercozoan assemblages in faecal samples are as diverse as those found in more conventionally examined habitats. These results reveal many novel lineages, some of which appear to occur preferentially in faecal material, in particular cercomonads and glissomonads. More broadly, we show that faecal habitats are likely untapped reservoirs of microbial eukaryotic diversity.

Protozoan Predation of Escherichia coli O157:H7 Is Unaffected by the Carriage of Shiga Toxin-Encoding Bacteriophages

Escherichia coli O157:H7 is a food-borne bacterium that causes hemorrhagic diarrhea and hemolytic uremic syndrome in humans. While cattle are a known source of E. coli O157:H7 exposure resulting in human infection, environmental reservoirs may also be important sources of infection for both cattle and humans. Bacteriophage-encoded Shiga toxins (Stx) carried by E. coli O157:H7 may provide a selective advantage for survival of these bacteria in the environment, possibly through their toxic effects on grazing protozoa. To determine Stx effects on protozoan grazing, we co-cultured Paramecium caudatum, a common ciliate protozoon in cattle water sources, with multiple strains of Shiga-toxigenic E. coli O157:H7 and non-Shiga toxigenic cattle commensal E. coli. Over three days at ambient laboratory temperature, P. caudatum consistently reduced both E. coli O157:H7 and non-Shiga toxigenic E. coli populations by 1-3 log cfu. Furthermore, a wild-type strain of Shiga-toxigenic E. coli O157:H7 (EDL933) and isogenic mutants lacking the A subunit of Stx 2a, the entire Stx 2a-encoding bacteriophage, and/or the entire Stx 1-encoding bacteriophage were grazed with similar efficacy by both P. caudatum and Tetrahymena pyriformis (another ciliate protozoon). Therefore, our data provided no evidence of a protective effect of either Stx or the products of other bacteriophage genes on protozoan predation of E. coli. Further research is necessary to determine if the grazing activity of naturally-occurring protozoa in cattle water troughs can serve to decrease cattle exposure to E. coli O157:H7 and other Shiga-toxigenic E. coli.

Effect of Neem (Azadirachta indica) on the Survival of Escherichia coli O157:H7 in Dairy Manure

Escherichia coli O157:H7 (EcO157) shed in cattle manure can survive for extended periods of time and intervention strategies to control this pathogen at the source are critical as produce crops are often grown in proximity to animal raising operations. This study evaluated whether neem (Azadirachta indica), known for its antimicrobial and insecticidal properties, can be used to amend manure to control EcO157. The influence of neem materials (leaf, bark, and oil) on the survival of an apple juice outbreak strain of EcO157 in dairy manure was monitored. Neem leaf and bark supplements eliminated the pathogen in less than 10 d with a D-value (days for 90% elimination) of 1.3 d. In contrast, nearly 4 log CFU EcO157/g remained after 10 d in neem-free manure control. The ethyl acetate extractable fraction of neem leaves was inhibitory to the growth of EcO157 in LB broth. Azadirachtin, a neem product with insect antifeedant properties, failed to inhibit EcO157. Application of inexpensive neem supplements to control pathogens in manure and possibly in produce fields may be an option for controlling the transfer of foodborne pathogens from farm to fork.

Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice

Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes.

Strain differences in fitness of Escherichia coli O157:H7 to resist protozoan predation and survival in soil

Escherichia coli O157:H7 (EcO157) associated with the 2006 spinach outbreak appears to have persisted as the organism was isolated, three months after the outbreak, from environmental samples in the produce production areas of the central coast of California. Survival in harsh environments may be linked to the inherent fitness characteristics of EcO157. This study evaluated the comparative fitness of outbreak-related clinical and environmental strains to resist protozoan predation and survive in soil from a spinach field in the general vicinity of isolation of strains genetically indistinguishable from the 2006 outbreak strains. Environmental strains from soil and feral pig feces survived longer (11 to 35 days for 90% decreases, D-value) with Vorticella microstoma and Colpoda aspera, isolated previously from dairy wastewater; these D-values correlated (P<0.05) negatively with protozoan growth. Similarly, strains from cow feces, feral pig feces, and bagged spinach survived significantly longer in soil compared to clinical isolates indistinguishable by 11-loci multi-locus variable-number tandem-repeat analysis. The curli-positive (C⁺) phenotype, a fitness trait linked with attachment in ruminant and human gut, decreased after exposure to protozoa, and in soils only C⁻ cells remained after 7 days. The C⁺ phenotype correlated negatively with D-values of EcO157 exposed to soil (r_s = −0.683; P = 0.036), Vorticella (r_s = −0.465; P = 0.05) or Colpoda (r_s = −0.750; P = 0.0001). In contrast, protozoan growth correlated positively with C⁺ phenotype (Vorticella, r_s = 0.730, P = 0.0004; Colpoda, r_s = 0.625, P = 0.006) suggesting a preference for consumption of C⁺ cells, although they grew on C⁻ strains also. We speculate that the C⁻ phenotype is a selective trait for survival and possibly transport of the pathogen in soil and water environments.

Rapid detection of predation of Escherichia coli O157:H7 and sorting of bacterivorous Tetrahymena by flow cytometry

Protozoa are known to harbor bacterial pathogens, alter their survival in the environment and make them hypervirulent. Rapid non-culture based detection methods are required to determine the environmental survival and transport of enteric pathogens from point sources such as dairies and feedlots to food crops grown in proximity. Grazing studies were performed on a soil isolate of Tetrahymena fed green fluorescent protein (GFP) expressing Escherichia coli O157:H7 to determine the suitability of the use of such fluorescent prey bacteria to locate and sort bacterivorous protozoa by flow cytometry. In order to overcome autofluorescence of the target organism and to clearly discern Tetrahymena with ingested prey vs. those without, a ratio of prey to host of at least 100:1 was determined to be preferable. Under these conditions, we successfully sorted the two populations using short 5–45 min exposures of the prey and verified the internalization of E. coli O157:H7 cells in protozoa by confocal microscopy. This technique can be easily adopted for environmental monitoring of rates of enteric pathogen destruction vs. protection in protozoa.