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Article: The Diversity and Abundance of Soft Rot Pectobacteriaceae Along the Durance River Stream in the Southeast of France Revealed by Multiple Seasonal Surveys

Ben Moussa, Hajar / Bertrand, Claire / Rochelle-Newall, Emma / Fiorini, Sarah / Pédron, Jacques / Barny, Marie-Anne

Phytopathology. 2022 Aug., v. 112, no. 8

2022

Abstract: Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot Pectobacteriaceae ...

Abstract	Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot Pectobacteriaceae (SRP) of the genera Dickeya and Pectobacterium over 2 years in a temperate, mixed-use watershed. The abundance of isolated strains correlates with the agricultural gradient along the watershed with a positive correlation found with temperature, nitrate, and dissolved organic carbon water concentration. We characterized 582 strains by amplification and sequencing of the gapA gene. Multilocus sequence analysis, performed with three housekeeping genes for 99 strains, and core genome analysis of 38 sequenced strains, confirmed for all the strains but one, the taxonomic assignation obtained with the sole gapA sequence. Pectobacterium spp. (549 isolates) were far more abundant than Dickeya spp. (33 isolates). Dickeya spp. were only observed in the lower part of the river when water temperature was >19°C, and we experimentally confirmed a decreased fitness of several Dickeya spp. at 8°C in river water. D. oryzae dominates the Dickeya spp. and P. versatile and P. aquaticum dominate the Pectobacterium spp., but their repartition along the watershed was different, with P. versatile being the only species regularly recovered all along the watershed. Excepting P. versatile, the Dickeya and Pectobacterium spp. responsible for disease outbreak on crops were less abundant or rarely detected. This work sheds light on the various ecological behaviors of different SRP types in stream water and indicates that SRP occupation is geographically structured.
Keywords	Dickeya ; Pectobacterium ; disease outbreaks ; irrigation water ; multilocus sequence typing ; nitrates ; occupations ; plant pathology ; river water ; rivers ; streams ; water temperature ; watersheds ; France
Language	English
Dates of publication	2022-08
Size	p. 1676-1685.
Publishing place	The American Phytopathological Society
Document type	Article
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-12-21-0515-R
Database	NAL-Catalogue (AGRICOLA)

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Article: Overland flow during a storm event strongly affects stream water chemistry and bacterial community structure

Le, Huong T. / Pommier, Thomas / Ribolzi, Olivier / Soulileuth, Bounsamay / Huon, Sylvain / Silvera, Norbert / Rochelle-Newall, Emma

Aquatic sciences. 2022 Jan., v. 84, no. 1

2022

Abstract: As flood events are expected to become more frequent due to climate change, investigating how overland flow exports terrestrial nutrients, carbon and living organisms into aquatic systems is essential for understanding both soil and stream ecosystem ... ...

Abstract	As flood events are expected to become more frequent due to climate change, investigating how overland flow exports terrestrial nutrients, carbon and living organisms into aquatic systems is essential for understanding both soil and stream ecosystem status. Here we assessed how dissolved organic carbon (DOC), total suspended sediments (TSS), and stream bacterial diversity responded to stream discharge and overland flow during stormflow in a tropical catchment. A higher humification index and a decreasing ratio of allochthonous to autochthonous DOC indicated that DOC from soils was exported to stream during the flood. The δ¹³C and δ¹⁵N of particulate matter was indicative of a source in the cultivated areas of the upper catchment and of subsurface soils (stream banks and gullies) in the downstream section. Bacterial richness of particle-attached (PA) and the free-living (FL) fractions increased with the flood progression in the upstream section. Moreover, the community structure of the PA fraction in the stream was more similar to that of overland flow than was the FL fraction. This suggests that the soil PA bacterial community was washed-out with overland flow during the flood recession. The relative contribution of sources and the composition of TSS, rather than hydrological regime, significantly drove the composition of bacterial community. In conclusion, our results emphasize that overland flow during a flood event strongly influences the structure of stream bacterial communities further underlining the biological connectivity between terrestrial runoff and stream flow.
Keywords	bacterial communities ; climate change ; community structure ; ecosystems ; humification ; hydrochemistry ; overland flow ; particulates ; runoff ; soil ; storms ; stream flow ; streams ; watersheds
Language	English
Dates of publication	2022-01
Size	p. 7.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	1464021-1
ISSN	1420-9055 ; 1015-1621
ISSN (online)	1420-9055
ISSN	1015-1621
DOI	10.1007/s00027-021-00839-y
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Article ; Online: Village Settlements in Mountainous Tropical Areas, Hotspots of Fecal Contamination as Evidenced by

Boithias, Laurie / Jardé, Emilie / Latsachack, Keooudone / Thammahacksa, Chanthanousone / Silvera, Norbert / Soulileuth, Bounsamay / Xayyalart, Mose / Viguier, Marion / Pierret, Alain / Rochelle-Newall, Emma / Ribolzi, Olivier

Environmental science & technology

2024 Volume 58, Issue 14, Page(s) 6335–6348

Abstract: Fecal bacteria in surface water may indicate threats to human health. Our hypothesis is that village settlements in tropical rural areas are major hotspots of fecal contamination because of the number of domestic animals usually roaming in the alleys and ...

Abstract	Fecal bacteria in surface water may indicate threats to human health. Our hypothesis is that village settlements in tropical rural areas are major hotspots of fecal contamination because of the number of domestic animals usually roaming in the alleys and the lack of fecal matter treatment before entering the river network. By jointly monitoring the dynamics of
MeSH term(s)	Humans ; Animals ; Environmental Monitoring ; Escherichia coli ; Water Microbiology ; Chickens ; Water Pollution ; Water ; Feces
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2024-03-26
Publishing country	United States
Document type	Journal Article
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.3c09090
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Metal contamination, their ecological risk, and relationship with other variables in surface sediments of urban rivers in a big city in Asia: case study of Hanoi, Vietnam.

Phung, Thi Xuan Binh / Le, Thi Phuong Quynh / Da Le, Nhu / Hoang, Thi Thu Ha / Nguyen, Thi Mai Huong / Rochelle-Newall, Emma / Nguyen, Thi Anh Huong / Duong, Thi Thuy / Pham, Thi Mai Huong / Nguyen, Tien Dat

Environmental science and pollution research international

2024 Volume 31, Issue 15, Page(s) 22362–22379

Abstract: Urban rivers are significantly impacted by anthropogenic pressure. This study presents the updated assessment of the concentrations of 11 metals and other variables (pH, total organic carbon (TOC) and nutrients (total nitrogen, total phosphorus, and ... ...

Abstract	Urban rivers are significantly impacted by anthropogenic pressure. This study presents the updated assessment of the concentrations of 11 metals and other variables (pH, total organic carbon (TOC) and nutrients (total nitrogen, total phosphorus, and total silica)) in the sediments of four urban rivers in inner Hanoi city, Vietnam, during the period 2020-2022. The mean concentrations of Fe, Zn, As, and Cr were higher than the permissible values of the Vietnam National technical regulation on the surface sediment quality. Moreover, Zn and Cr were at the severe effect level of the US EPA guidelines for sediment quality. The calculation of pollution indices (I
MeSH term(s)	Metals, Heavy/analysis ; Vietnam ; Rivers ; Water Pollutants, Chemical/analysis ; Geologic Sediments ; Environmental Monitoring/methods ; Asia ; Risk Assessment ; China
Chemical Substances	Metals, Heavy ; Water Pollutants, Chemical
Language	English
Publishing date	2024-02-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-024-32549-x
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Article: The Diversity and Abundance of Soft Rot

Ben Moussa, Hajar / Bertrand, Claire / Rochelle-Newall, Emma / Fiorini, Sarah / Pédron, Jacques / Barny, Marie-Anne

Phytopathology

2022 Volume 112, Issue 8, Page(s) 1676–1685

Abstract	Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot
MeSH term(s)	France ; Gammaproteobacteria ; Pectobacterium/genetics ; Plant Diseases/microbiology ; Rivers ; Seasons ; Water
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2022-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-12-21-0515-R
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Article: Spatio-temporal dynamics of suspended particulate matter in the middle Niger River using in-situ and satellite radiometric measurements

Boubacar Moussa, Moussa / Abdourhamane Touré, Amadou / Kergoat, Laurent / Lartiges, Bruno / Rochelle-Newall, Emma / Robert, Elodie / Gosset, Marielle / Alkali Tanimoun, Bachir / Grippa, Manuela

Journal of hydrology. 2022 June, v. 41

2022

Abstract: Study Region: Middle Niger River Basin (MNRB), Ansongo to Niamey, Sahel, West Africa. Study Focus: Although MNRB hydrology and the red flood phenomena have been addressed in the past literature, water quality parameters and suspended particulate matter ( ... ...

Abstract	Study Region: Middle Niger River Basin (MNRB), Ansongo to Niamey, Sahel, West Africa. Study Focus: Although MNRB hydrology and the red flood phenomena have been addressed in the past literature, water quality parameters and suspended particulate matter (SPM) dynamics remain poorly known. SPM impacts dam silting, exacerbating flooding, and microbial water quality. This study couples in-situ SPM measurements to radiometric measurements by in-situ and satellite sensors to analyse the temporal and spatial evolution of SPM in the MNRB and assess the contribution of the local flood (red flood) to SPM in Niamey. New Hydrological Insights for the Region: SPM is composed of very fine kaolinites with a major mode around 200–300 nanometers which results in high reflectance in the visible and infrared bands. Radiometric measurements by both radiometer and Sentinel-2 MSI sensors are well correlated to in-situ SPM, allowing efficient spatio-temporal monitoring of SPM concentration. SPM increases very rapidly at the beginning of the rainy season, reaching a peak, characterized by very high SPM values, about one month before the red flood. Satellite data highlight the significant contribution of the right bank tributaries to SPM in the MNRB during this period. SPM then decreases and remains low despite the second runoff increase (black flood) arriving in Niamey after the end of the rainy season from the upper basin.
Keywords	Sahel ; basins ; particulates ; radiometry ; reflectance ; remote sensing ; rivers ; runoff ; satellites ; water quality ; watersheds ; wet season ; Western Africa
Language	English
Dates of publication	2022-06
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2814784-4
ISSN	2214-5818
ISSN	2214-5818
DOI	10.1016/j.ejrh.2022.101106
Database	NAL-Catalogue (AGRICOLA)

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Article: Land use strongly influences soil organic carbon and bacterial community export in runoff in tropical uplands‐

Le, Huong T / Rochelle‐Newall, Emma / Ribolzi, Olivier / Janeau, Jean Louis / Huon, Sylvain / Latsachack, Keooudone / Pommier, Thomas

Land degradation & development. 2020 Jan. 15, v. 31, no. 1

2020

Abstract: Rapid development and associated land‐use change have resulted in increased soil erosion and widespread land degradation in tropical ecosystems. Precipitation‐induced soil erosion causes the export of soil organic carbon (SOC) and the associated ... ...

Abstract	Rapid development and associated land‐use change have resulted in increased soil erosion and widespread land degradation in tropical ecosystems. Precipitation‐induced soil erosion causes the export of soil organic carbon (SOC) and the associated bacterial community affecting soil quality and functioning. We assessed the transfer of SOC and soil bacterial diversity and functions in surface water runoff from different land uses: Teak with and without understory (TW and TWO, respectively) and upland rice (UR) in a tropical, upland catchment during a simulated rain event. Total suspended sediment (TSS) concentration was higher in TWO (1.23 ± 0.21 g L−1) than in TW (0.37 ± 0.16 g L−1) and UR (0.44 ± 0.2 g L−1), whereas dissolved organic carbon (DOC) concentration was lower under TWO (3.8 ± 0.7 mg L−1) than under TW or UR (13.4 ± 7.5 and 9.57 ± 4.8 mg L−1, respectively). Runoff from TWO harboured the highest proportion of bacterial taxa common to soil (27% and 29.5%) as compared with TW (22.8% and 13%) and UR (17.3% and 7%) for both particle attached and free‐living fractions, respectively. Bacterial community export in surface runoff was driven by changes in DOC and TSS, suggesting that eroded soil particles simultaneously carry organic carbon and attached bacterial taxa in surface runoff. Consequently, the export of soil functional groups relating to organic carbon degradation and nitrogen cycle was higher under TWO than in TW or UR. Our results underline that teak plantations with unsustainable practices such as the removal of understory degrades soil functions and accelerates land degradation through soil erosion and surface runoff on the long term.
Keywords	Tectona grandis ; bacterial communities ; biodiversity ; dissolved organic carbon ; ecosystems ; eroded soils ; highlands ; land degradation ; land use change ; losses from soil ; nitrogen cycle ; plantations ; rainfall simulation ; rice ; runoff ; soil bacteria ; soil erosion ; soil organic carbon ; soil quality ; surface water ; suspended sediment ; understory ; watersheds
Language	English
Dates of publication	2020-0115
Size	p. 118-132.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1319202-4
ISSN	1085-3278
ISSN	1085-3278
DOI	10.1002/ldr.3433
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Environmental determinants of E. coli, link with the diarrheal diseases, and indication of vulnerability criteria in tropical West Africa (Kapore, Burkina Faso).

Robert, Elodie / Grippa, Manuela / Nikiema, Dayangnéwendé Edwige / Kergoat, Laurent / Koudougou, Hamidou / Auda, Yves / Rochelle-Newall, Emma

PLoS neglected tropical diseases

2021 Volume 15, Issue 8, Page(s) e0009634

Abstract: In 2017, diarrheal diseases were responsible for 606 024 deaths in Sub-Saharan Africa. This situation is due to domestic and recreational use of polluted surface waters, deficits in hygiene, access to healthcare and drinking water, and to weak ... ...

Abstract	In 2017, diarrheal diseases were responsible for 606 024 deaths in Sub-Saharan Africa. This situation is due to domestic and recreational use of polluted surface waters, deficits in hygiene, access to healthcare and drinking water, and to weak environmental and health monitoring infrastructures. Escherichia coli (E. coli) is an indicator for the enteric pathogens that cause many diarrheal diseases. The links between E. coli, diarrheal diseases and environmental parameters have not received much attention in West Africa, and few studies have assessed health risks by taking into account hazards and socio-health vulnerabilities. This case study, carried out in Burkina Faso (Bagre Reservoir), aims at filling this knowledge gap by analyzing the environmental variables that play a role in the dynamics of E. coli, cases of diarrhea, and by identifying initial vulnerability criteria. A particular focus is given to satellite-derived parameters to assess whether remote sensing can provide a useful tool to assess the health hazard. Samples of surface water were routinely collected to measure E. coli, enterococci and suspended particulate matter (SPM) at a monitoring point (Kapore) during one year. In addition, satellite data were used to estimate precipitation, water level, Normalized Difference Vegetation Index (NDVI) and SPM. Monthly epidemiological data for cases of diarrhea from three health centers were also collected and compared with microbiological and environmental data. Finally, semi-structured interviews were carried out to document the use of water resources, contact with elements of the hydrographic network, health behavior and condition, and water and health policy and prevention, in order to identify the initial vulnerability criteria. A positive correlation between E. coli and enterococci in surface waters was found indicating that E. coli is an acceptable indicator of fecal contamination in this region. E. coli and diarrheal diseases were strongly correlated with monsoonal precipitation, in situ SPM, and Near Infra-Red (NIR) band between March and November. Partial least squares regression showed that E. coli concentration was strongly associated with precipitation, Sentinel-2 reflectance in the NIR and SPM, and that the cases of diarrhea were strongly associated with precipitation, NIR, E. coli, SPM, and to a lesser extent with NDVI. Moreover, E. coli dynamics were reproduced using satellite data alone, particularly from February to mid-December (R2 = 0.60) as were cases of diarrhea throughout the year (R2 = 0.76). This implies that satellite data could provide an important contribution to water quality monitoring. Finally, the vulnerability of the population was found to increase during the rainy season due to reduced accessibility to healthcare and drinking water sources and increased use of water of poor quality. During this period, surface water is used because it is close to habitations, easy to use and free from monetary or political constraints. This vulnerability is aggravated by marginality and particularly affects the Fulani, whose concessions are often close to surface water (river, lake) and far from health centers.
MeSH term(s)	Burkina Faso/epidemiology ; Diarrhea/epidemiology ; Diarrhea/microbiology ; Diarrhea/prevention & control ; Escherichia coli/isolation & purification ; Feces/microbiology ; Humans ; Hygiene ; Rain ; Seasons ; Water Microbiology ; Water Pollution ; Water Quality ; Water Supply
Language	English
Publishing date	2021-08-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2727
ISSN (online)	1935-2735
ISSN	1935-2727
DOI	10.1371/journal.pntd.0009634
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Article: Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns

David, Gwendoline M / López‐García, Purificación / Moreira, David / Alric, Benjamin / Deschamps, Philippe / Bertolino, Paola / Restoux, Gwendal / Rochelle‐Newall, Emma / Thébault, Elisa / Simon, Marianne / Jardillier, Ludwig

Molecular ecology. 2021 May, v. 30, no. 9

2021

Abstract: Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water ... ...

Abstract	Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri‐annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2–9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2‐year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.
Keywords	Archaea ; bacterial communities ; biodiversity ; climate change ; community structure ; eukaryotic cells ; freshwater ; genes ; greenhouses ; seasonal variation ; surveys ; water quality ; France
Language	English
Dates of publication	2021-05
Size	p. 2162-2177.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.15864
Database	NAL-Catalogue (AGRICOLA)

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Article: Experimental and modelling evidence of splash effects on manure borne Escherichia coli washoff

Mügler, Claude / Ribolzi, Olivier / Viguier, Marion / Janeau, Jean-Louis / Jardé, Emilie / Latsachack, Keooudone / Henry-Des-Tureaux, Thierry / Thammahacksa, Chanthamousone / Valentin, Christian / Sengtaheuanghoung, Oloth / Rochelle-Newall, Emma

Environmental science and pollution research. 2021 July, v. 28, no. 25

2021

Abstract: In tropical montane South-East Asia, recent changes in land use have induced increased runoff, soil erosion and in-stream suspended sediment loads. Land use change is also contributing to increased microbial pathogen dissemination and contamination of ... ...

Abstract	In tropical montane South-East Asia, recent changes in land use have induced increased runoff, soil erosion and in-stream suspended sediment loads. Land use change is also contributing to increased microbial pathogen dissemination and contamination of stream waters. Escherichia coli (E. coli) is frequently used as an indicator of faecal contamination. Field rain simulations were conducted to examine how E. coli is exported from the surface of upland, agricultural soils during runoff events. The objectives were to characterize the loss dynamics of this indicator from agricultural soils contaminated with livestock waste, and to identify the effect of splash on washoff. Experiments were performed on nine 1 m² plots, amended or not with pig or poultry manure. Each plot was divided into two 0.5 m² sub-plots. One of the two sub-plots was protected with a mosquito net for limiting the raindrop impact effects. Runoff, soil detachment by raindrop impact and its entrainment by runoff, and E. coli loads and discharge were measured for each sub-plot. The results show that raindrop impact strongly enhances runoff generation, soil detachment and entrainment and E. coli export. When the impact of raindrops was reduced with a mosquito net, total runoff was reduced by more than 50%, soil erosion was on average reduced by 90% and E. coli export from the amended soil surface was on average 3 to 8 times lower. A coupled physics-based approach was performed using the Cast3M platform for modelling the time evolutions of runoff, solid particles detachment and transfer and bacteria transport that were measured for one of the nine plots. After estimation of the saturated hydraulic conductivity, soil erodibility and attachment rate of bacteria, model outputs were consistent with measured runoff coefficients, suspended sediment and E. coli loads. This work therefore underlines the need to maintain adequate vegetation at the soil surface to avoid the erosion and export of soil borne potential pathogens towards downstream aquatic systems.
Keywords	Escherichia coli ; erodibility ; exports ; highlands ; land use change ; mosquito nets ; pathogens ; poultry manure ; rain ; raindrop impact ; research ; runoff ; saturated hydraulic conductivity ; sediments ; soil amendments ; soil erosion ; streams ; suspended sediment ; swine ; vegetation ; South East Asia
Language	English
Dates of publication	2021-07
Size	p. 33009-33020.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-021-13011-8
Database	NAL-Catalogue (AGRICOLA)

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