Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils DOI Creative Commons
Zhi-Bo Zhao, Ji‐Zheng He, Stefan Geisen

et al.

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Feb. 27, 2019

Agricultural food production is at the base of and fodder, with fertilization having fundamentally continuously increased crop yield over last decades. The performance crops intimately tied to their microbiome as they together form holobionts. importance for plant is, however, notoriously ignored in agricultural systems disconnects dependency plants often plant-beneficial microbial processes. Moreover, we lack a holistic understanding how regimes affect soil microbiome. Here, examined effect 2-year regime (no nitrogen control, fertilization, plus straw amendment) on entire microbiomes (bacteria, fungi, protist) three common types cropped maize two seasons.We found that application fertilizers more strongly affected protist than bacterial fungal communities. Nitrogen indirectly reduced diversity through changing abiotic properties communities which differed between sampling seasons. fertilizer amendment had greater effects physicochemical addition alone. even straw, network complexity, suggesting tightened interactions.Together, our results suggest protists are most susceptible component fertilizers. As also exhibit strongest seasonal dynamics, serve sensitive bioindicators changes. Changes might have long-term if some key hubs govern complexities top predators altered. This study serves stepping stone promote promising agents targeted engineering help reducing exogenous unsustainably high pesticide applications.

Language: Английский

Keystone taxa as drivers of microbiome structure and functioning DOI
Samiran Banerjee, Klaus Schlaeppi, Marcel G. A. van der Heijden

et al.

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(9), P. 567 - 576

Published: May 22, 2018

Language: Английский

Citations

2098
Bacteria and archaea on Earth and their abundance in biofilms DOI
Hans‐Curt Flemming,

Stefan Wuertz

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(4), P. 247 - 260

Published: Feb. 13, 2019

Language: Английский

Citations

1335
Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning DOI Creative Commons
Cameron Wagg, Klaus Schlaeppi, Samiran Banerjee

et al.

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Oct. 24, 2019

Abstract The soil microbiome is highly diverse and comprises up to one quarter of Earth’s diversity. Yet, how such a functionally complex influences ecosystem functioning remains unclear. Here we manipulated the in experimental grassland ecosystems observed that diversity microbial network complexity positively influenced multiple functions related nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed networks reduced richness had lowest multifunctionality due fewer taxa present support same function (redundancy) lower different (reduced functional uniqueness). Moreover, explained pointing significance communities. These findings indicate importance interactions within among fungal bacterial communities for enhancing performance demonstrate extinction ecological associations belowground can impair functioning.

Language: Английский

Citations

1217
A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application DOI Creative Commons
Stéphane Compant, Abdul Samad, Hanna Faist

et al.

Journal of Advanced Research, Journal Year: 2019, Volume and Issue: 19, P. 29 - 37

Published: March 20, 2019

Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount information is now available on the structure dynamics microbiota as well functional capacities isolated community members. Due to interesting potential due current challenges in crop production there an urgent need bring microbial innovations into practice. Different approaches microbiome improvement exist. On one hand strains or strain combinations can be applied, however, field success often variable urgently required. Smart, knowledge-driven selection needed use suitable delivery formulations. other hand, farming practices genotype influence thus functioning. Therefore, appropriate breeding leading improved plant-microbiome interactions are avenues increase benefit microbiota. In conclusion, different making new generation inoculants application microbiome-based agro-management lines could lead better microbiome. This paper reviews importance functionalities bacterial discusses concepts regard plant-associated bacteria.

Language: Английский

Citations

1107
Soil carbon storage informed by particulate and mineral-associated organic matter DOI
Maurizio Cotrufo, Maria Giovanna Ranalli, Michelle L. Haddix

et al.

Nature Geoscience, Journal Year: 2019, Volume and Issue: 12(12), P. 989 - 994

Published: Nov. 18, 2019

Language: Английский

Citations

1086
Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots DOI Creative Commons
Samiran Banerjee, Florian Walder, Lucie Büchi

et al.

The ISME Journal, Journal Year: 2019, Volume and Issue: 13(7), P. 1722 - 1736

Published: March 8, 2019

Root-associated microbes play a key role in plant performance and productivity, making them important players agroecosystems. So far, very few studies have assessed the impact of different farming systems on root microbiota it is still unclear whether agricultural intensification influences structure complexity microbial communities. We investigated conventional, no-till, organic wheat fungal communities using PacBio SMRT sequencing samples collected from 60 farmlands Switzerland. Organic harbored much more complex network with significantly higher connectivity than conventional no-till systems. The abundance keystone taxa was highest under where lowest. also found strong negative association (R2 = 0.366; P < 0.0001) between connectivity. occurrence best explained by soil phosphorus levels, bulk density, pH, mycorrhizal colonization. majority are known to form arbuscular associations plants belong orders Glomerales, Paraglomerales, Diversisporales. Supporting this, fungi roots soils farming. To our knowledge, this first study report for agroecosystems, we demonstrate that reduces microbiome.

Language: Английский

Citations

953
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses DOI Creative Commons
Jiarong Guo, Benjamin Bolduc, Ahmed A. Zayed

et al.

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Feb. 1, 2021

Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, insufficiently advanced identification tools.Here, we introduce VirSorter2, DNA RNA virus tool that leverages genome-informed advances across collection customized automatic classifiers improve accuracy range detection. When benchmarked against genomes from both isolated uncultivated viruses, VirSorter2 uniquely performed consistently with high (F1-score > 0.8) viral diversity, while all other tools under-detected viruses outside group represented reference databases (i.e., those order Caudovirales). Among evaluated, was also able minimize errors associated atypical cellular sequences including eukaryotic plasmids. Finally, as virosphere exploration unravels novel sequences, VirSorter2's modular design makes it inherently expand new types via maintain maximal sensitivity specificity.With multi-classifier design, demonstrates higher overall major groups will advance our knowledge evolution, virus-microbe interaction various ecosystems. Source code is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), on bioconda an iVirus app CyVerse https://de.cyverse.org/de ). Video abstract.

Language: Английский

Citations

815
Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change DOI Creative Commons
Ashish Malik, Jennifer B. H. Martiny, Eoin Brodie

et al.

The ISME Journal, Journal Year: 2019, Volume and Issue: 14(1), P. 1 - 9

Published: Sept. 25, 2019

Microorganisms are critical in terrestrial carbon cycling because their growth, activity and interactions with the environment largely control fate of recent plant inputs as well protected soil organic [1, 2]. Soil stocks reflect a balance between microbial decomposition stabilisation assimilated carbon. The can shift under altered environmental conditions [3], new research suggests that knowledge physiology may be for projecting changes improving prognosis climate change feedbacks [4–7]. Still, predicting ecosystem implications processes remains challenge. Here we argue this challenge met by identifying life history strategies based on an organism’s phenotypic characteristics, or traits, representing these models. What key traits change? Microbial growth survival impacted multiple determine responses to varying resource availability fluctuating abiotic [8]. Cellular maintenance activities (those do not produce growth) include production extracellular enzymes degrade acquire resources, biomolecular repair mechanisms, cellular integrity, osmotic balance, defence, antagonism, cell signalling motility [9–11]. It is conceivable investment into would generally high soils, highly heterogeneous temporally variable distribution stressful like extremes moisture, temperature, pH salinity [12, 13]. Selective pressures suboptimal could lead greater cellular-level physiological allocation relative (Fig. 1) thereby impacting processes. Open separate window Fig. 1 Schematic showing C flux includes depolymerisation, substrate uptake, assimilation, dissimilation, biomass synthesis non-growth production. Extracellular enzyme represents acquisition, stress protein linked tolerance reflects higher yield. Forked arrows signify metabolic points where hypothesised tradeoffs might occur. expected empirical relationships among also shown

Language: Английский

Citations

725
Bacterial siderophores in community and host interactions DOI
Jos Kramer, Özhan Özkaya, Rolf Kümmerli

et al.

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 18(3), P. 152 - 163

Published: Nov. 20, 2019

Language: Английский

Citations

721
Land use driven change in soil pH affects microbial carbon cycling processes DOI Creative Commons
Ashish Malik, Jérémy Puissant, Kate M. Buckeridge

et al.

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Aug. 29, 2018

Abstract Soil microorganisms act as gatekeepers for soil–atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding mechanisms responsible hinders development effective land management strategies to enhance storage. Here we empirically test link between microbial ecophysiological traits topsoil content across geographically distributed soils use contrasts. We discovered distinct pH controls on accumulation. Land intensification in low-pH that increased above a threshold (~6.2) leads loss through decomposition, following alleviation acid retardation growth. with near-neutral was linked decreased biomass reduced growth efficiency was, turn, related trade-offs stress resource acquisition. Thus, less-intensive practices have more potential storage efficiency, whereas acidic soils, is bigger constraint decomposition rates.

Language: Английский

Citations

674