Mineralization of soil colloids by aerobic heterotrophic bacteria of soils

134 Pages·2017·3.89 MB·English

by  Olga Drozdova

Mineralization of soil colloids by aerobic heterotrophic
bacteria of soils
Olga O. Drozdova
To cite this version:
Olga O. Drozdova. Mineralization of soil colloids by aerobic heterotrophic bacteria of soils. Applied
geology. Universite Toulouse III Paul Sabatier, 2015. English. ￿NNT: ￿. ￿tel-01273306￿
HAL Id: tel-01273306
https://theses.hal.science/tel-01273306
Submitted on 12 Feb 2016
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Acknowledgements
This PhD thesis has been elaborated from October 2011 till September 2015 between the
University Paul Sabatier of Toulouse, France, and the Moscow State University, Russia, within
the French government scholarship programme for a double supervised dissertation.
I would like to address my acknowledgements to my scientific directors, the heads of
projects and co-authors of the publications for the offered topic for this thesis, for their
professional supervision and for giving me their support in all the time of research and writing of
this thesis - Oleg S. Pokrovsky, Galina М. Motuzova, Ludmila S. Shirokova, Vladimir V.
Demin, Aridane González, Ilina S.M. and Sergey A. Lapitskiy. I would also like to thank the
technical and engineering staffs of GET and of the Moscow State University for the help with
my experiments and analysis - Carole Causserand, Aurélie Lanzanova, Jonathan Prunier, Manuel
Henry and Yuliya A. Zavgorodnyaya. I would like to thank the opponents of this thesis - Andrey
Yu. Bichkov and Sergey N. Kirpotin, for having accepted to judge my work.
I thank all my family for their support, patience and faith in me.
And finally, I would also like to thank everybody who was important to the successful
realization of thesis, as well as expressing my apology that I could not mention personally one by
one.
I would like to mention that this work was supported by grant BIO-GEO-CLIM
(Resolution of RF Government No. 220, Agreement No. 14.В25.31.0001) and grants for Basic
Research and CNRS (Grants №№ 12-04-31796-mol_а, 11-05-00464_a, 11-05-93111-CNRS_a,
14-05-0430_a).
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Contents

Abstract……………………………………………………………………...5
Résumé………………………………………………………………………6
Введение…………………………………………………………………….7
Chapter 1. General introduction………………………………………………9
1.1. Background of the study…………………………………………………………..10
1.2. Study site…………………………………………………………………………..14
1.3. Objects of the study………………………………………………………………..15
1.4. Thesis organisation………………………………………………………………...16
Chapter 2. Decrease in zinc adsorption onto soil in the presence of EPS-rich
and EPS-poor Pseudomonas aureofaciens ……………………………………………20
2.1. Introduction…………………………………………………………………………...23
2.2. Materials and methods………………………………………………………………..25
2.2.1. Soil samples…………………………………………………………………………………..25
2.2.2. Culture characterization……………………………………………………………………26
2.2.3 Metal adsorption……………………………………………………………………………..26
2.2.4. Lineal Programming Model (LPM)……………………………………………………….27
2.3. Results and Discussion………………………………………………………………..29
2.3.1. DOC concentration in adsorption experiments………………………………………….29
2.3.2. Adsorption of zinc as a function of the pH……………………………………………….31
2.3.3. Adsorption of zinc as a function of the zinc concentration in solution……………….35
2.3.4. Linear-programming modeling……………………………………………………………40
2.4. Conclusions……………………………….…………………………………………..41
Chapter 3. Impact of heterotrophic bacterium Pseudomonas aureofaciens
on the release of major and trace elements from podzol soil into aqueous solution...48
3.1. Introduction…………………………………………………………………………...51
3.2. Materials and methods………………………………………………………………..53
3.2.1. Soils, bacteria, experiments and analyses………………………………………….…….53
3.2.2. Data treatment and statistics…………………………………………………………….…55
3.3. Results………………………………………………………………………………....57
3.3.1. Bacteria, pH, DOC and DIC concentration……………………………………………...57
3.3.2. Released concentrations as a function of time and element classification……….…..60
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3.3.2.1. Silica and alkaline/alkaline-earth elements (Si, Mg, K, Ca, Sr, Ba, Rb)………61
3.3.2.2. Divalent heavy metals (Cu, Mn, Zn, Ni, Cd, Pb)………………………………….65
3.3.2.3. Phosphorus and oxyanions…………………………………………………………..67
3.3.2.4. Trivalent and tetravalent hydrolysates……………………………………………..68
3.4. Discussion……………………………………………………………………………..70
3.4.1. Processes controlling element release during soil interactions
with aqueous solutions………………………………………………………………………….…..70
3.4.1.1. pH changes during the experiment and various pools of metals in soils………71
3.4.1.2. Metal complexation with DOC, EPS production and
heterotrophic consumption of organic complexes………………………………………….76
3.4.1.3. TE adsorption on bacterial surfaces and bacterial intracellular uptake………76
3.4.2. Application to natural environments………………………………………………………77
3.5. Conclusions …………………………………………………………………………...80
Chapter 4. Size fractionation and optical properties of dissolved organic matter
in the continuum soil solution-bog-river and terminal lake of a boreal watershed…92
4.1. Introduction……………………………………………………………………… …...95
4.2. Site description…………………………………………………………………… …..97
4.3. Material and methods……………………………………………………………… …98
4.3.1. Sampling, filtration……………………………………………………………………… ….98
4.3.2. Analytical techniques……………………………………………………………………… 101
4.4. Results and discussion……………………………………………………………… ..102
4.4.1. General hydrochemical parameters…………………………………………………… …102
4.4.2. Representativity of the samples………………………………………………………… …103
4.4.3. Spatial variation in OC characteristics……………………………………………… …..105
4.4.3.1. DOC concentration………………………………………………………………… ..105
4.4.3.2. C/N ratio…………………………………………………………………………… ….105
4.4.3.3. Optical characteristics…………………………………………………………… ….106
4.4.4. Size fractionation of DOM……………………………………………………………… ….107
4.4.4.1. DOC concentration pattern…………………………………………………… …….107
4.4.4.2. MW distribution from size exclusion chromatography…………………… ……..111
4.4.4.3. C/N as an indicator of OM origin…………………………………………… ……..112
4.4.4.4. Optical characteristics of DOM………………………………………………. ..…..113
4.5. Conclusions ………..………………………………..…………………………… …...116
Chapter 5. Conclusions and perspectives……………………………………….……..130
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Abstract
It is known that global climate change has an impact on all components of the
hydrobiogeochemical ecological systems. This is especially true for high-latitude boreal
ecosystems that are exposed these changes are stronger than others. It is necessary to study these
cycles in uncontaminated systems for to understand and quantitatively predict human disturbance
of biogeochemical cycles of elements. Among the different regions of the world, the boreal region
are one of the largest reservoirs of organic carbon in the peat and soil (organic rich). The release
of organic carbon and metals, due to permafrost thawing, and increased runoff of Arctic river
(which induced global warming) are likely to change the forms of elements in soil solutions and
waters of the rivers and their number that falls falls into the ocean. This is a very important
scientific environmental problem.
Multidisciplinary approach for the study of the biogeochemical cycles of the main elements
in soils and waters controlled by the activity of microorganisms (by uptake/release of cells or in
the process of degradation of dissolved organic matter) was used in the thesis. The innovation of
this work is to study the effect of microbial activity (soil typical aerobic bacteria Pseudomonas)
on the biogeochemical cycles of elements due to take place geochemical, physical, chemical and
microbiological processes. The simultaneous study of the biogeochemical cycles of elements and
parameters of biological activity will allow us to predict the response of natural systems to
climate change and human-induced disturbance (organic or metallic contamination).
Field studies were accompanied by detailed laboratory studies of the reaction mechanisms.
The thesis considers to the study of physical and chemical processes using of experimental
modeling of the degradation of organic matter in soil extracts and to the study of the quantitative
relation between the degradation of organic matter by heterotrophic bacteria Pseudomonas and
cycles elements.

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Résumé
On sait que les changements globaux climatiques constituent des forçages qui s’exercent
sur toutes les composantes hydrobiogéochimiques des systèmes écologiques. Ceci est
particulièrement vrai pour les écosystèmes boréaux de haute latitude qui sont des régions très
fragiles, fortement soumises au réchauffement climatique. Afin de comprendre et prédire de
manière quantitative les perturbations d’origine anthropique des cycles biogéochimiques, il est
urgent d’acquérir la connaissance de ces cycles dans les systèmes non pollués «pristines», encore
non (ou peu) perturbés. Parmi les différentes régions de monde, les zones boréales représentent
un des plus importants réservoirs de carbone organique sous forme de tourbières ou de sols très
riches en matière organique. La libération du carbone organique et des métaux en trace associés
durant le dégel du permafrost, induite par le réchauffement climatique, constitue le principal
changement que subit ce milieu et le principal enjeu scientifique et environnemental.
L’augmentation continue du débit des rivières arctiques au cours des dernières décennies,
combinée à la libération du carbone et des métaux piégés dans le permafrost, est susceptible de
modifier les flux d’éléments vers les océans, mais aussi la spéciation de ces dernières dans les
eaux de rivière ou les solutions de sol.
Cette thèse s’inscrit dans une approche résolument pluridisciplinaire, centrée sur l’étude
biogéochimique des cycles d’éléments majeurs – éléments en trace dans les eaux contrôlées par
l’activité des microorganismes (piégeage/rélargage par la biomasse ou dégradation de la matière
organique dissoute et particulaire). Le caractère innovant de сette thèse réside dans l’étude, pour
la première fois, de l’impact de l’activité microbienne (minéralisation aerobiques par les
bactéries typiques des sols, Pseudomonas) sur les cycles biogéochimiques des éléments grâce à
la mise en œuvre en parallèle d’outils géochimiques, physico-chimiques et microbiologiques.
Cette étude simultanée des cycles biogéochimiques des éléments et des paramètres d’activité
biologique nous permettra de prédire les réponses des systèmes naturels aux changements
climatiques et aux interventions humaines (sous forme de pollution organique ou métallique).
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Les études de terrain ont été accompagnés par des étude plus detaillés en laboratoire des
mécanismes réactionnels. Dans le cadre de ce travail, mes efforts ont été consacrés à l'étude
physico-chimique des processus via la modélisation expérimentale de la dégradation de la
matière organique des extraits du sol. Et des recherches des relations quantitatives entre la
dégradation de la matière organique par les bactéries hétérotrophes Pseudomonas et les cycles
des éléments associés.

Введение
Известно, что глобальное изменение климата оказывает влияние на все
биогеохимические компоненты экологических систем. Это особенно верно для
высокоширотных бореальных экосистем, которые сильнее других подвергаются этим
изменениям. Чтобы понять и количественно предсказать антропогенные нарушения
биогеохимических циклов элементов, необходимо изучать эти циклы в незагрязненных
системах, что на данный момент мало исследовано. Среди различных регионов мира,
бореальная зона представляет собой один из крупнейших резервуаров органического
углерода в торфе и почве, богатой органическими веществами. Высвобождение
органического углерода и металлов при таянии вечной мерзлоты и увеличение
арктического речного стока в последние десятилетия, связанные с глобальным
потеплением, скорее всего, изменит формы нахождения элементов в почвенных растворах
и водах рек и их количества, попадающих в океаны. Это является очень важной научной
экологической проблемой.
В диссертации развивается междисциплинарный подход, в центре которого
находится изучение биогеохимических циклов основных элементов в почвах и водах,
контролируемых жизнедеятельностью микроорганизмов (путем захвата/освобождения
клетками или в процессе деградации растворенного органического вещества). Научная
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новизна данной работы заключается в исследовании влияния микробной активности
(типичных почвенных аэробных бактерий Pseudomonas) на биогеохимические циклы
элементов вследствие происходящих параллельно геохимических, физико-химических и
микробиологических процессов. Одновременное изучение биогеохимических циклов
элементов и параметров биологической активности позволит нам предсказать ответ
природных систем на изменение климата и антропогенное вмешательство (в виде
загрязнения органическими веществами и металлами).
Полевые исследования сопровождались более детальными лабораторными
исследованиями механизмов реакций. Диссертация, в основном, посвящена изучению
физических и химических процессов, с помощью экспериментального моделирования
деградации органического вещества в почвенных экстрактах. А также исследованию
количественного соотношения между деградацией органического вещества
гетеротрофными бактериями Pseudomonas и циклами, связанных с ним элементов.
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