Cattle manure application triggers short-term dominance of Acinetobacter in soil microbial communities

Pérez-Valera, Eduardo; Rangel, Wesley de Melo; Elhottová, Dana

doi:10.1016/j.apsoil.2022.104466

Cited by 10 publications

(4 citation statements)

References 58 publications

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“…Both of them were often found as the main phyla in soils [ 51 , 52 ]. After the dairy manure application, the bacterial community structure in the soil was significantly changed by increasing the relative abundance of Firmicutes and Bacteroidetes , consistent with previous findings [ 53 ]. Firmicutes and Bacteroidetes had been widely reported as the predominant phyla in cattle manure, both accounted for approximately 70% of the bacterial community in some cattle fecal samples [ 3 , 54 ].…”

Section: Discussionsupporting

confidence: 90%

“…In agreement with previous findings [ 24 ], we found such shifts are rapid. The humid environment might facilitate the spread of microorganisms from manure to the soil [ 53 ], and the nutrients in manure such as the content of nitrogen and organic carbon could promote the proliferation of certain bacteria in soil [ 51 ]. The incubation period, not the addition of antibiotics, was the primary factor for the temporal shifts of the bacteria community in soil.…”

Section: Discussionmentioning

confidence: 99%

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Shifts of Antibiotic Resistomes in Soil Following Amendments of Antibiotics-Contained Dairy Manure

Kang

Liu

Chen

et al. 2022

IJERPH

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Dairy manure is a nutrition source for cropland soils and also simultaneously serves as a contamination source of antibiotic resistance genes (ARGs). In this study, five classes of antibiotics including aminoglycosides, beta-lactams, macrolides, sulfonamides, and tetracyclines, were spiked in dairy manure and incubated with soil for 60 days. The high throughput qPCR and 16S rRNA amplicon sequencing were used to detect temporal shifts of the soil antibiotic resistomes and bacterial community. Results indicated dairy manure application increased the ARG abundance by 0.5–3.7 times and subtype numbers by 2.7–3.7 times and changed the microbial community structure in soils. These effects were limited to the early incubation stage. Selection pressure was observed after the addition of sulfonamides. Bacterial communities played an important role in the shifts of ARG profiles and accounted for 44.9% of the resistome variation. The incubation period, but not the different antibiotic treatments, has a strong impact on the bacteria community. Firmicutes and Bacteroidetes were the dominant bacterial hosts for individual ARGs. This study advanced our understanding of the effect of dairy manure and antibiotics on the antibiotic resistome in soils and provided a reference for controlling ARG dissemination from dairy farms to the environment.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Shifts of Antibiotic Resistomes in Soil Following Amendments of Antibiotics-Contained Dairy Manure

Kang

Liu

Chen

et al. 2022

IJERPH

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“…Understanding how soil bacterial communities react to continuous fertilization is crucial for directing the development of an effective rice field fertilization plan. Prior studies have reported that continued fertilization of organic manure alone or combined with CF can increase soil microbial communities’ diversity and abundance and improve soil quality ( Kumar et al, 2017 ; Cui et al, 2018 ; Pérez-Valera et al, 2022 ). Appropriate manure application can regulate the soil microbial community and improve the soil’s micro-ecological environment ( Ikoyi et al, 2020 ; Li T. et al, 2020 ; Hou et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Partial Substation of Organic Fertilizer With Chemical Fertilizer Improves Soil Biochemical Attributes, Rice Yields, and Restores Bacterial Community Diversity in a Paddy Field

Iqbal

Ali

et al. 2022

Front. Plant Sci.

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Conventional farming systems are highly reliant on chemical fertilizers (CFs), which adversely affect soil quality, crop production and the environment. One of the major current challenges of current agriculture is finding ways to increase soil health and crop yield sustainably. Manure application as a substitute for CF is an alternative fertilization strategy for maintaining soil health and biodiversity. However, little is known about the complex response of soil bacterial communities and soil nutrients to manure and CFs application. This study reports the response of soil nutrients, rice yield, and soil microbial community structure to 2 years of continuous manure and CFs application. The study consisted of six treatments: no N fertilizer control (Neg-Con); 100% CF (Pos-Con); 60% cattle manure (CM) + 40% CF (High-CM); 30% CM + 70% CF (Low-CM); 60% poultry manure (PM) + 40% CF (High-PM), and 30% PM + 70% CF (Low-PM). We used high-throughput sequencing of 16S ribosomal RNA gene amplicons to characterize the soil bacterial communities. Results revealed that the addition of manure significantly altered the soil bacterial community composition and structure; and enhanced the relative abundance of phyla Proteobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Planctomycetes. Organic fertilizer treatments, particularly high CM and PM had the highest measured soil bacterial diversity of all treatments. Similarly, integrated application of manure and CFs increased the soil biochemical traits [i.e., pH, total N (TN), soil organic C (SOC), microbial biomass N (MBN), and microbial biomass C (MBC)] and rice grain yield. Average increases in SOC, TN, MBN, and MBC were 43.66, 31.57, 24.34, and 49.45%, respectively, over the years in the High-PM compared with Pos-Con. Redundancy analysis showed that the dominant bacteria phyla were correlated with soil pH, SOC, TN, and microbial biomass, but the relative abundance of Proteobacteria was strongly correlated with environmental factors such as soil pH, SOC, TN, and MBC. We employed a structural equation model to examine the relationship between microbial biomass, soil nutrients and grain yield among treatments. This analysis supported the hypothesis that soil nutrient content and availability directly affect rice grain yield while soil bacteria indirectly affect grain yield through microbial biomass production and nutrient levels. Overall, the findings of this research suggest that the integrated application of CF and manure is a better approach for improving soil health and rice yield.

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“…Several studies resolved on the level of the genus Acinetobacter illustrate the marked position of Acinetobacter species at the beginning of a succession. Aging of cattle and chicken manure correlates with a characteristic burst and decline of Acinetobacter (17, 84, 92). In line, Acinetobacter has been described to dominate the rice paddy rhizosphere after green manure treatment in comparison to winter fallow treatment (137).…”

Section: Discussionmentioning

confidence: 99%

On the ecology ofAcinetobacter baumannii– jet stream rider and opportunist by nature

Wilharm,

Skiebe,

Łopińska

et al. 2024

Preprint

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The natural reservoirs of the nosocomial pathogen Acinetobacter baumannii are not well defined. We previously identified white storks as a model system to study the ecology of A. baumannii. Having screened more than 1,300 white stork nestlings over a period of six years across different regions of Poland and Germany (overall isolation rate of ~29.5%), including food chain analyses and environmental samplings, we come up with a detailed picture of the dynamics and diversity of A. baumannii in their natural habitats. Adult storks, rather than being stably colonized with strains of A. baumannii which are successively transferred to their offspring, instead initially encounter these bacteria while foraging. Among their common food sources, consisting of earthworms, small mammals, and insects, we identified earthworms as a potential source of A. baumannii, but more so the associated soil as well as plant roots. Through this, hotspot soil and compost habitats were identified which enable population dynamics to be studied over the course of the year. We demonstrate that sterilized plant material is rapidly colonized by airborne A. baumannii suggesting they patrol to search for novel habitats, being opportunist by nature. The prevalence of A. baumannii exhibited a strong seasonality and peaked during summer. The strains we collected in Poland and Germany represent more than 50% of the worldwide known diversity in terms of the intrinsic OXA-51-like beta-lactamase. A set of ~400 genomes was determined and compared to a diverse set of publicly available genomes. Our pan-genome estimate of the species (~51,000 unique genes) more than doubles the amount proposed by previous studies. Core-genome based phylogenetic analyses illustrated numerous links between wildlife isolates and hospital strains, including ancient as well as recent intercontinental transfer. Our data further suggest massive radiation within the species early after its emergence, matching with human activity during the Neolithic. Deforestation in particular seemed to set the stage for this bloom as we found that forests do not provide conducive conditions for the proliferation of A. baumannii. In contrast, wet and nutrient-rich soil alongside rivers sampled during the summer can yield an isolation rate of ~30%. Linking published work on the interaction between A. baumannii and fungi and on aspergillosis as a major cause of mortality in white stork nestlings to our findings, we hypothesized that fungi and A. baumannii share a long history of coevolution. Interaction studies revealed the capability of A. baumannii to adhere to fungal spores and to suppress spore germination. Taken together, the intrinsic resistance endowment and potential to acquire antibiotic resistance can be explained by coevolution with antibiotic-producing fungi and other microorganisms within soil, and resistance to desiccation stress and radiation can be interpreted in the light of intercontinental hitchhiking through fungal spores.

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Cattle manure application triggers short-term dominance of Acinetobacter in soil microbial communities

Cited by 10 publications

References 58 publications

Shifts of Antibiotic Resistomes in Soil Following Amendments of Antibiotics-Contained Dairy Manure

Shifts of Antibiotic Resistomes in Soil Following Amendments of Antibiotics-Contained Dairy Manure

Partial Substation of Organic Fertilizer With Chemical Fertilizer Improves Soil Biochemical Attributes, Rice Yields, and Restores Bacterial Community Diversity in a Paddy Field

On the ecology ofAcinetobacter baumannii– jet stream rider and opportunist by nature

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