Tillage practices can influence soil microbial carbon use efficiency (CUE), which is critical for carbon cycling in terrestrial ecosystems. The effect of tillage practices could also be regulated by ...nitrogen (N) addition. However, the soil microbial mechanism relating to N fertilizer effect on microbial CUE under no‐tillage (zero‐tillage) is still unclear. We investigated how N fertilizer regulates the effect of tillage management on microbial CUE through changing microbial properties and further assessed the impact of microbial CUE on particulate (POC) and mineral‐associated organic matter carbon (MAOC). For this we used a 16‐year field experiment with no‐tillage (NT) and conventional tillage (CT), both of which combined with 105 (N1), 180 (N2), and 210 kg N ha−1 (N3) N application. We found that microbial CUE increased with increasing N application rate. NT increased microbial CUE compared with CT in the 0–10 cm. The bacterial and fungal diversities of NT were higher than CT and N application decreased their diversities in 0–10 cm. The partial least squares path model showed that bacterial and fungal diversity had a significant influence on microbial CUE. Furthermore, POC and MAOC under NT were higher than CT and they also increased with increasing N application rate. It suggested that increasing microbial CUE induced by N application had the potential to increase POC and MAOC. Overall, this study highlights that N addition can alter the effect of soil microbial diversity on CUE, which further improves our understanding to explain and predict the fractions of SOC (i.e., POC and MAOC) in tillage systems.
Microbial oceanography of anoxic oxygen minimum zones Ulloa, Osvaldo; Canfield, Donald E; DeLong, Edward F ...
Proceedings of the National Academy of Sciences - PNAS,
10/2012, Volume:
109, Issue:
40
Journal Article
Peer reviewed
Open access
Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen ...economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N ₂) and nitrous oxide (N ₂O) gases. Anaerobic microbial processes, including the two pathways of N ₂ production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two “end points” represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.
The long-term fate of plastics in the ocean and their interactions with marine microorganisms remain poorly understood. In particular, the role of sinking plastic particles as a transport vector for ...surface microbes towards the deep sea has not been investigated. Here, we present the first data on the composition of microbial communities on floating and suspended plastic particles recovered from the surface to the bathypelagic water column (0-2000 m water depth) of the North Pacific Subtropical Gyre. Microbial community composition of suspended plastic particles differed from that of plastic particles afloat at the sea surface. However, in both compartments, a diversity of hydrocarbon-degrading bacteria was identified. These findings indicate that microbial community members initially present on floating plastics are quickly replaced by microorganisms acquired from deeper water layers, thus suggesting a limited efficiency of sinking plastic particles to vertically transport microorganisms in the North Pacific Subtropical Gyre.
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•Differential microbial communities on floating versus submerged plastic particles in the North Pacific Subtropical Gyre•Plastic sinking from surface waters towards the underlying deep sea provides only a limited transport for surface microbial communities•Hydrocarbon-degrading bacteria colonize plastic particles in surface and subsurface waters•Subsurface plastic particles harbor a more specialized microbial community than plastic particles afloat at the sea surface
Microbial diversity associated with coffee quality.
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•Coffee production requires complex procedures that affect both production and quality.•Microorganisms influence coffee growth and ...chemical profile.•Bioprospecting of coffee-associated microorganisms and metabolites can enhance sensory profiles.•Microorganisms can generate new sensory profiles through targeted fermentations.
Coffee stands as one of the world's most popular beverages, and its quality undergoes the influence of numerous pre- and post-harvest procedures. These encompass genetic variety, cultivation environment, management practices, harvesting methods, and post-harvest processing. Notably, microbial communities active during fermentation hold substantial sway over the ultimate quality and sensory characteristics of the final product. The interaction between plants and microorganisms assumes critical significance, with specific microbes assuming pivotal roles in coffee plant growth, fruit development, and, subsequently, the fruit's quality. Microbial activities can synthesize or degrade compounds that influence the sensory profile of the beverage. However, studies on the metabolic products generated by various coffee-related microorganisms and their chemical functionality, especially in building sensory profiles, remain scarce. The primary aim of this study was to conduct a literature review, based on a narrative methodology, on the current understanding of the plant-microorganism interaction in coffee production. Additionally, it aimed to explore the impacts of microorganisms on plant growth, fruit production, and the fermentation processes, directly influencing the ultimate quality of the coffee beverage. Articles were sourced from ScienceDirect, Scopus, Web of Science, and Google Scholar using specific search terms such as “coffee microorganisms”, “microorganisms-coffee interactions”, “coffee fermentation”, “coffee quality”, and ‘coffee post-harvest processing”. The articles used were published in English between 2000 and 2023. Selection criteria involved thoroughly examining articles to ensure their inclusion was based on results about the contribution of microorganisms to both the production and quality of the coffee beverage. The exploration of microorganisms associated with the coffee plant and its fruit presents opportunities for bioprospecting, potentially leading to targeted fermentations via starter cultures, consequently generating new profiles. This study synthesizes existing data on the current understanding of the coffee-associated microbiome, its functionalities within ecosystems, the metabolic products generated by microorganisms, and their impacts on fermentation processes and grain and beverage quality. It highlights the importance of plant-microorganism interactions in the coffee production chain.
The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite ...their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape‐scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. We found that variation in soil microbial communities was explained by abiotic factors like climate, pH and soil properties. Biotic factors, namely community‐weighted means (CWM) of plant functional traits, also explained variation in soil microbial communities. In particular, more bacterial‐dominated microbial communities were associated with exploitative plant traits versus fungal‐dominated communities with resource‐conservative traits, showing that plant functional traits and soil microbial communities are closely related at the landscape scale.
A laboratory study was conducted to evaluate the impact of bioaugmentation plus biostimulation (BR, added both nutrients and bacterial consortia), and natural attenuation (NA) on hydrocarbon ...degradation efficiency and microflora characterization during remediation of a freshly contaminated soil. After 112 days of remediation, the initial level of total petroleum hydrocarbon (TPH) (61,000 mg/kg soil) was reduced by 4.5% and 5.0% in the NA and BR treatments, respectively. Bioremediation did not significantly enhance TPH biodegradation compared to natural attenuation. The degradation of the aliphatic fraction was the most active with the degradation rate of 30.3 and 28.7 mg/kg/day by the NA and BR treatments, respectively. Soil microbial activities and counts in soil were generally greater for bioremediation than for natural attenuation. MiSeq sequencing indicated that the diversity and structure of microbial communities were affected greatly by bioremediation. In response to bioremediation treatment, Promicromonospora, Pseudomonas, Microcella, Mycobacterium, Alkanibacter, and Altererythrobacter became dominant genera in the soil. The result indicated that combining bioaugmentation with biostimulation did not improve TPH degradation, but soil microbial activities and structure of microbial communities are sensitive to bioremediation in short-term and heavily oil-contaminated soil.
•An increase in aromatics and abatement of polar hydrocarbons were observed.•Bioremediation increased the α-diversity and activities of soil microorganisms.•The typical petroleum degrading bacteria were abundant in response to remediation.•Exotic consortia did not perform well in the short-term contaminated soil.
The atmosphere as a temporary habitat for airborne microbial communities is a valuable topic to explore, and it is through aerobiological studies that the diversity of biological particles and their ...release, emission, transport, deposition, and impact are assessed. Specific microorganisms are involved in meteorological processes, and phytosanitary and public health concerns. Airborne microbial composition is related to factors such as geographic region and weather conditions.
In this study a metagenomic approach was used to determine the composition of bacterial and fungal communities in the air of two different land-use areas (urban area and semi-rural area), during dry and rainy seasons in Mexico City. Air sampling was carried out with a Hirst-type spore trap, collecting the samples simultaneously in both study areas. Forty-two bioaerosol samples were collected, and the DNA obtained was sequenced using Next-Generation Sequencing. The results indicated that the bacterial communities were represented mainly by the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria, and the fungal communities by the phyla Ascomycota followed by Basidiomycota. The evident changes in microbial composition were related more to seasonality than to locality, since both UA and SRA showed a high degree of urbanization, despite some differences in land use. Continuous monitoring of atmospheric bioaerosols is essential to determine the influence of meteorological factors on the composition of the aerial microbiota.
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•Aerobiological studies should be considered in air quality monitoring.•Seasonal variations are the main factor related to changes in the composition of the bacterial and fungal communities.•The Semi-Rural Area showed greater airborne bacterial richness than the Urban Area.•The Urban Area showed greater airborne fungal richness than the Semi-Rural Area.•Airborne bacteria and fungi were represented mainly by Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria and by Ascomycota and Basidiomycota.
Although many studies have reported the negative effects of elevated O
on plant physiological characteristics, the influence of elevated O
on below-ground processes and soil microbial functioning is ...less studied. In this study, we examined the effects of elevated O
on soil properties, soil microbial biomass, as well as microbial community composition using high-throughput sequencing. Throughout one growing season, one-year old seedlings of two important endemic trees in subtropical China: Taxus chinensis (Pilger) Rehd. var. chinensis, and Machilus ichangensis Rehd. Et Wils, were exposed to charcoal-filtered air (CF as control), 100 nl l
(E100) or 150 nl l
(E150) O
-enriched air, in open top chambers (OTCs). We found that only higher O
exposure (E150) significantly decreased soil microbial biomass carbon and nitrogen in M. ichangensis, and the contents of organic matter were significantly decreased by E150 in both tree species. Although both levels of O
exposure decreased NO
-N in T. chinensis, only E150 increased NO
-N in M. ichangensis, and there were no effects of O
on NH
-N. Moreover, elevated O
elicited changes in soil microbial community structure and decreased fungal diversity in both M. ichangensis and T. chinensis. However, even though O
exposure reduced bacterial diversity in M. ichangensis, no effect of O
exposure on bacterial diversity was detected in soil grown with T. chinensis. Our results showed that elevated O
altered the abundance of bacteria and fungi in general, and in particular reduced nitrifiers and increased the relative abundance of some fungal taxa capable of denitrification, which may stimulate N
O emissions. Overall, our findings indicate that elevated O
not only impacts the soil microbial community structure, but may also exert an influence on the functioning of microbial communities.
•Existence of alternative microbiota states in rivers were identified by field data.•NH4+−N and NO3−−N were identified as main environmental stress.•Clostridiales, Nitrospirales and Myxococcales were ...discerned as key taxa.•Alternative stable states theory can guide river biodiversity conservation.
Catastrophic shifts in river ecosystems can abruptly degrade their structures and functions, often reducing the efficacy of traditional remediation targeting physicochemical properties. Alternative stable states theory can not only explain this phenomenon but also provide a new insight into river restoration; however, little is known about the existence and implications of alternative stable states in a river. Considering the important role of benthic microbiota in sustaining river ecosystem structures and functions, ecological theory and high-throughput sequencing were combined to firstly investigate multi-stability in microbial communities and its relationship with environmental factors in river sediments. The Nanjing reach of the Yangtze River was selected as the study area because of its huge spatial heterogeneity and varying degrees of pollution. Bimodal distributions combined with temporal variations of microbiota status provided direct evidence of bistability by showing the instability at the intermediate. In addition, environmental stress, particularly concentrations of NH4+−N and NO3−−N, was identified as an important driver of alternative microbiota states from the perspectives of the behavior of bistable ecosystems. Comparison of α-diversity indices and network properties between two alternative microbiota states revealed that the diversity and co-occurrence pattern of microbial communities will be high if they are settled in favorable environments (i.e., comprehensive sediment quality identification index > 3.7). Key taxa, including Clostridiales, Nitrospirales and Myxococcales, were discerned by combining LEfSe and network analysis, and their strong interspecies interactions were believed to be an important factor in triggering alternative microbiota states. This study suggests alternative stable states theory should be considered in river remediation to better understand the response of river ecosystems to environmental stress and the effect of hysteresis, benefiting the implementation of effective monitoring and restoration strategies in a river of urban area.
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Both soil properties and plant root traits are pivotal factors affecting microbial communities. However, there is still limited information about their importance in shaping rhizosphere soil ...microbial communities, particularly in less-studied alpine shrub ecosystems. To investigate the effects of altitude (3300, 3600, 3900, and 4200 m) on the diversity and composition of rhizosphere soil bacterial and fungal communities, as well as the factors shaping rhizosphere soil microbial communities, we conducted this study in alpine Rhododendron nitidulum shrub ecosystems from the Zheduo mountain of the eastern Tibetan Plateau. Results demonstrated that bacterial community diversity and richness decreased to the lowest value at 3600 m and then increased at higher altitudes compared with 3300 m; whereas fungal richness at 3300 m was much lower than at other altitudes, and was closely related to soil properties and root traits. The composition of rhizosphere soil bacterial and fungal communities at the low altitude (3300 m) was different from that at high altitudes. Permutational multivariate analysis of variance and redundancy analysis indicated that soil properties (soil water content, pH, NO3−-N, and available phosphorus) and root traits (surface area, and maximum depth) were the major factors explaining the variations of rhizosphere soil bacterial and fungal communities. Specific bacterial and fungal taxa along altitudes were identified. The bacterial taxa Planctomycetota was dominant at 3300 and 3600 m with low soil nutrient availability and high root surface area, whereas the fungal taxa Mortierellomycota was abundant at 3900 and 4200 m with high soil nutrient availability and low root surface area. These results suggested that different soil microbes can respond differently to altitude. This study provides a novel insight into factors driving rhizosphere soil bacterial and fungal community variations, which could improve our understanding of microbial ecology in alpine R. nitidulum shrub ecosystems along altitude.
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•Rhizosphere soil bacterial and fungal alpha-diversity and community structure varied along altitudes.•Rhizosphere soil microbial alpha-diversity was related closely with soil properties.•Rhizosphere soil microbial community variations were mainly affected by soil properties and root traits of host plant.•The responses to altitude of soil microbes varied with microbial taxa.
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