Postal address: Institutionen för geologiska vetenskaper, Svante Arrhenius väg 8 C, SE-106 91 Stockholm, Sweden
Visiting address: Frescati University Campus, Earth Sciences Center, House R, 4th floor
Web page: http://www.geo.su.se/index.php/en

Contact person: Alaisdair Skelton, Professor of Geochemistry and Petrology, phone: +46 (0)8 16 47 50

Biogeochemistry is an interdisciplinary science combining the disciplines of microbiology and geology to interpret the intricate traces left behind by living organisms in sedimentary rocks from earlier stages of our planet’s history. Many environmental problems of today are related to biogeochemistry. Microbes acting in waste material either accentuate them or microbes can be used in measures used to lower or eliminate pollution problems. At the section of Biogeochemistry research projects in paleo- as well as recent biogeochemistry have been carried out.

The department is also part of the Bolin Centre for Climate Research at Stockholm University. More information.

Research related to South Asia:

• Professor Alasdair Skelton has been involved in several research project related to India. He has collaborated with Dr. Chandan Mohanta at the Indian Institute of Technology, IIT, in Guwahati, India (read SASNET’s report from a visit to Dr. Mohanta’s department at IIT Guwahati, November 2005).
The project deals with prediction of earthquakes, and is called ”Monitoring the effect of seismic activity on groundwater chemistry in NE India”. It received a three-years Swedish Research Links grant from Sida and the Swedish Research Council in November 2005. The project aimed at finding means of accurately predicting earthquakes by studying the seismic activities in North East India, an extremely vulnerable area where a major earthquake is expected to hit the region in the near future.

In November 2013, the Swedish Research Council decided to give Dr. Christophe Sturm, Senior Lecturer in Biogeochemical modeling, SEK 4.076 million as a three-year (2014-16) U-forsk grant for a project entitled ”Past-present-future Monsoon Variability Revealed by Stable Water Isotopes: Combining Observations and Climate Models to Assess its Impacts on Bhutan and Nepal”, to be carried out in collaboration with Dr.  Qiong Zhang at the Dept. of Physical Geography and Quaternary Geology. In South Asia the research partners are:
– Norbu Wangdi, Department of Water Resources, Ugyen Wangchuk Institute for Conservation and Environment (UWICE), Bumtang, Bhutan; 
– Moti L. Rijal, Department of Watershed Management and Environmental Sciences, Institute of Forestry, Tribhuvan University, Kathmandu, Nepal; Naoyuki Kurita, Department of Earth and Environmental Sciences, Nagoya University, Japan; and 
– Patrick Wagnon, International Centre for Integrated Mountain Development (ICIMOD), Kathmandu, Nepal.
 More information about the South Asia related U-forsk grants 2013.

• For several years, Dr Joyanto Routh worked in the Section for Biogeochemistry, but he has now moved to the Department of Water and Environmental Studies, Tema Institute, Linköping University. 
Dr. Routh has carried out research on Arsenic mobilization in the environment. Since the onset of the green revolution during 1970’s in south-east Asia, increased paddy cultivation and drinking water supply necessitated the use of groundwater in large quantities. Since then, groundwater development has increased multifold over the past three decades to sustain the need of groundwater for irrigation and safe drinking water. Unfortunately, these groundwaters have high arsenic (As) levels, which have resulted in a severe environmental catastrophe. The first reports on the clinical manifestations of As toxicity in the Bengal Delta Plain (BDP) region (Bangladesh and India) turned up around 1978, and thereafter, chronic As poisoning cases were reported in 1982-83. Today the problem is very critical and over 70 million people in Bangladesh and India are drinking groundwater orders of magnitude higher then the WHO specified limits for As (10 ppb).

Dr. Routh has been involved in the research project Arsenic in the Bengal Delta Plain Groundwaters in West Bengal (India) – Genesis and Mitigation Aspects: An interdisciplinary research proposal for investigating arsenic contamination in groundwater and remediation strategies, which was given a first Sida/SAREC planning project in 2002. The project was carried out in collaboration with the Groundwater Arsenic Research Group, GARG, Dept. of Land and Water Resources Engineering, Kungl Tekniska Högskolan, Stockholm.

In November 2004 he was again given a Sida/SAREC grant for a period of two years for this project now renamed ”In situ remediation of arsenic rich groundwater in Ambikanagar, West Bengal (India)”. More information.
In June 2005 Dr. Routh also received SEK 750 000 as a grant for two years from FORMAS research council for the same project (read the abstract, in Swedish), and in November 2005 he got a one-year research grant from Sida/SAREC for a project titled ”Microbial Arsenite oxidation: Implications on arsenic cycling in aquifer system”. More information on Sida funded South Asia related research projects in 2005.
Dr. Routh has continued to do research on arsenic rich groundwater in West Bengal. The main collaboration partner on the Indian side is Dr S P Sinha Ray from the Centre for Ground Water Studies in Kolkata. He is a leading expert on arsenic remediation in the country. He is also one of the members of the Arsenic Task Force – a special group of scientists, academics, and government officials constituted by the Government of West Bengal (India) to oversee the arsenic problem in the state.
The project has was launched in West Bengal in 2007, and focuses on treating the arsenic contaminated groundwater. The plant treats ca. 200 cubic metres of water daily and provides As-free groundwater to the local villagers.
In August 2008, SASNET awarded a guest lecture programme grant to Dr. Joyanto Routh (besides a planning grant for a new research project, see below). He was given SEK 20 000 in order to invite Dr. Ray from Kolkata to deliver a series of lectures on arsenic related issues in groundwater in Sweden. Dr Ray was co-invited by the Geological Survey of Sweden (SGU) in Stockholm; the Hydrology Section at Uppsala University; and the Division of Land and Water Resources Engineering, Royal Institute of Technology (KTH), Stockholm to give lectures at these institutions as well. More information about the SASNET planning grants 2008.

In August 2004 Routh was awarded a SASNET planning grant for a new project on ”Environmental and long-term pitfalls of human induced changes in lake ecosystems: A case study of the Kumaun Lakes in NE India”. See the full list of SASNET Planning grants recipients. The project was carried out in collaboration with Dr. G J Chakrapani, Indian Institute of Technology (IIT), Roorkee, and focused on the environmental deterioration of lakes in the Kumaun valley in northeast India. Their intent was to set up an interdisciplinary study investigating the changes in the watershed over the last 200 years, and the remedial measures that can be considered to ameliorate the situation. In October 2004, Joyantho Routh received SEK 600 000 as a Swedish Research Links three-years grant (Asian–Swedish research partnership programme) by Sida and the Swedish Research Council for this project now renamed ”Sedimentary record of human-induced environmental changes and affects in the Kumaun Lakes, India”, for the period 2005-07. More information.

Another project relates to Pichavaram Mangrove forest in South East India. In June 2005 Dr. Routh received SEK 675 000 as a two-years grant from the research council FORMAS for this project, dealing with nutritional and polluting sources and sedimentations; biogeochemical processes and effects in an undisturbed ecosystem. The project was carried out in collaboration with Associate Professor A.L. Ramanathan at Jawaharlal Nehru University (JNU) in New Delhi.
A PhD student from India, Rajesh Ranjan from JNU worked as an exchange student in Stockholm with Dr. Routh on this project. Mr. Ranjan was expected to defend his doctoral dissertation in 2009.
Project abstract (only in Swedish): Pichavaran mangroverna är belägena i sydöstra Indien. Deras läge i skyddade, vindstilla områden gör att fina partiklar, anrikade med tungmetaller, organiskt material och mineraler avsätts där. Dessa skogar är darför ideala områden för studier av naturliga och antropogena processer, omfattande blandning, upplösning, avdunstning och kemiskt utbyte mellan floder, havsvatten och sediment. Moderna studier visar en mycket intensiv primärproduktion och en accelererande nerbrytning i Pichvaran. Detta beror framför allt på antropogena aktiviteter. I denna undersökning kommer vi att använda geokemiska parametrar storskaligt och på molekylär nivå för att kunna förstå: 1) Det biogeokemiska uppträdandet och kretsloppet av näringsämnen och föroreningar. 2) Miljöförstöring och effekten på mangroveproduktiviteten och 3) för att spåra historiska förändringar och miljöstörningar under de senaste årtiondena. Studien kommer att omfatta talrika provtagningar, kemiska analyser av sediment och vattenprover (spårmetaller, organiska föreningar och isotoper), sedimentkronologi och geokemisk modellering.  

In November 2007, Dr. Joyanto Routh received SEK 1.2 million as a three years grant (2008-10) from Sida’s Developing Country Research Council (U-landsforskningsrådet) for a research project titled ”High-Resolution Lacustrine Records from the Thar Desert Playas in northwestern India: Reconstructing Regional Paleoclimate and Monsoon Patterns”. More information about the 2007 Sida grants.
The project was carried out in collaboration with Prof. Barbara Wohlfarth at the same department, and Prof. and Dr. Stefano Bernasconi at the Department of Earth Sciences, Swiss Federal Institute of Technology (ETH) in Zürich. The main collaboration partner on the South Asian side were Prof. Anil Gupta from Indian Institute of Technology (IIT) in Kharagpur.
Dr Narender Meena at Wadia Institute of Himalayan Geology also collaborates in this project.
Project abstract: The Indian Ocean Monsoon (IOM) has a critical role in the global climate, hydrological and energy cycles. The monsoons have repeatedly varied over time and affected the socio-economic life in the region. We will test the hypotheses: 1) strong southwest winds mean higher precipitation on land in summer, and 2) small amplitude changes in North Atlantic during the Holocene are accompanied by variations in the terrestrial record of IOM. Our goal is to reconstruct a high-resolution late-glacial to near-modern paleoclimatic record based on 14C ages, and geochemical proxies (biomarkers, isotopes, paleomagnetism, and elemental ratios). The proxies will relate IOM variability with vegetation and temperature. Our data will be correlated with the Arabian Sea and Chinese peat records. This study in the Sambhar and Didwana lakes in Rajasthan will be done in collaboration with researchers from India.

In August 2008, Dr. Routh was awarded a SASNET planning grant for a research projet titled ”Biogeochemical signatures and high-resolution paleoclimatic records in spelotherms from caves in Meghalaya (India)”. More information about the 2008 SASNET planning grants.
The project is carried out in collaboration with Dr. Ramanathan Baskar from the Dept. of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology in Hisar, Haryana, India. Dr. Susmitha Baskar from the same university also works with Dr. Routh on the project. She is supported by the Swedish Institute. She came to Sweden in July 2009, and stayed for 1,5 years to work as a post-doc researcher.
Reconaissance survey of these caves was conducted in February 2009 and sampling was done in three caves (Syndai, Rupasor, and Mawmluh). The group collected samples for various microbiological assays and geochemical analyses. In Novermber 2009, another short fieldtrip was done to collect fresh samples for geomicrobiological work. Collaboration was set up with Dr Natuschka Lee at Technical University Munich, Germany, to process the samples.
Various analyses were made during the summer 2009. Various microbes were isolated which were involved in precipitating carbonate minerals in the caves. The work was recently submitted to Geomicrobiology Journal and is currently under review.
Project abstract: Caves are open cavities in the earth serving as natural sediment traps. Caves have emerged as one of the frontiers in Earth System Science research to address challenging questions related to various biogeochemical processes. Information on geochemical processes in caves can be also used as proxies for reconstructing high-resolution paleoclimate records. In a recently started cooperative initiative between Stockholm University and Asian universities on interdisciplinary climate related research, we propose to investigate some caves in Meghalaya, northeast India. The primary scientific aims of this project are to: 1) do a reconnaissance of different cave systems in the Khasi and Jaintia Hills in Meghalaya, 2) focus on few of these caves for sampling drip water and speleothems, and 3) perform some preliminary investigations to determine the possibility of building long-term paleoclimate records. The study also focuses on capacity building measures including training and education with researchers from Guru Jambheshwar University of Science and Technology (India).

In November 2009, this project planned for by a SASNET grant, was awarded SEK 1.5 m as a three years grant (2010-12) from Sida’s Developing Country Research Council (U-landsforskningsrådet). The research project has now been renamed ”Asian monsoon variability and impacts on terrestrial ecosystems: High-resolution records in speleothem and lacustrine archives from northeast India”. More information about the 2009 Sida grant

In August 2009, Dr. Routh was awarded another SASNET planning grant for a new research project entitled ”High-resolution Holocene paleoclimate records in glacial lakes from the northeastern Himalayas in Bhutan”. More information about the 2009 SASNET planning grants.
The aim of this project is to initiate a reconnaissance study of accessible lake systems in the northeastern Bhutan Himalayas. Most of these glacial lakes directly lie in the path of the Indian summer monsoons and experience heavy rainfall. In addition, global warming has caused several of these glacial lakes to burst repeatedly posing danger for the local people and their property (Jaxa, 2009).Specifically, we address the hypotheses that sedimentary archives in these glacial lake systems preserve detailed information of climate change in the sub-continent. Till now there has been nothing published on the geology or geochemistry of these mountain lakes.

The researchers focused on the pristine Lake Jimilangtsho located on the famous Druk Path trek between Thimpu and Paro. It is situated in the Thimpu (Phajoding) district and takes around 7 days to reach from Thimpu. The lake is ca. 460 m in length and is 200 m in breadth. The lake lies in the upper catchment of the Paro Chhu River. The lake is oblong in shape and is fed by stream in the northern part of the lake. The blocking of the exit of the flow of water by big rocks and boulders on the southern site, possibly by a landslide, has led to the formation the lake. There is evidence of rock sliding and debris flow on the southwestern margin of the lake.
Fieldwork was carried out in October 2010 by a team from Örebro University (Joyanto Routh was affiliated to Örebro University during this period), the Department of Mines and Geology, Bhutan (Samten Wangdi) and the Department of Earth Sciences at the Indian Institute of Science Education and Research (IISER) in Kolkata (Rajarshi Roychoudharyand Manoj Jaiswal). The depth of the water column at the points where the cores were collected ranged from 8 to 10 m. Since the reconnaissance sampling was conducted in 2010, the following geochemical analyses were done in these sediments. This resulted in a MSc thesis by Rajarshi Roychoudhary, which was submitted to the Department of Earth Sciences, IISER-Kolkata in May 2012.
Read an activity report on the SASNET funded project.
As of June 2012, the researchers jointly work on a manuscript which they plan to submit after summer 2012. In addition, they are planning to submit a full proposal to research funding agencies to support their research initiatives with the Department of Mines and Geology at Bhutan in 2013. 

In December 2009, Dr. Routh received SEK 735 000 as a three-year International Collaborative Research Grant from the Swedish Research Links programme (funded by Sida and the Swedish Research Council) for a India related project entitled ”Arsenic biogeochemical cycling in groundwater aquifers of the Bengal Delta Plains (West Bengal, India): Early detection and remediation issues”. See the full list of South Asia related projects given Swedish Research Links grants 2009.
The research project will be carried out in collaboration with Dr. Punyasloke Bhadury, microbiologist at the Indian Institute of Science Education and Research (IISER) in Kolkata.
Project abstract: Arsenic toxicity is a global health problem affecting millions of people. The situation is most critical in the Bengal Delta Plains (BDP) affecting >70 million people in India and Bangladesh. Cost-affective early detection and suitable remediation schemes for As removal are mostly ineffective. Recent studies indicate that biogeochemical interactions and microbial processes play a crucial role in As cycling in the BDP aquifers. However, these issues are poorly understood and/ investigated, and affect of microbial processes are mostly restricted to laboratory studies. This novel interdisciplinary study focuses on: 1) isolation of indigenous microbial communities (As(III)- oxidizers) associated with As cycling and metabolism, and 2) development and evaluation of an integrated biochemical sensor that can detect As(III)- oxidizing bacteria, and corresponding As levels in groundwater. The project is located in Ambikanagar and Badkula – two small villages in West Bengal, which are impacted by high (up to 150 ppb) As levels in groundwater. Synergetic development and cooperation between the research groups (at Stockholm University and IISER-Kolkata) are expected to provide new insights for developing cost-affective As remediation techniques based on early detection and suitable bioaugmentation methods. Finally, outcome of this collaborative project is very desirable for sustainable use, development, and proper management of groundwater resources in the region.

Indian Guest lecturers at the department

Professor Govind J. Chakrapani from the Department of Earth Sciences, Indian Institute of Technology (IIT) Roorkee was a visiting professor at the department in the Summer 2007.
Prof. Chakrapani was the co-supervisor, along with Dr. Routh, for an Indian visiting PhD candidate, Preetam Choudhary, recruited from IIT Roorkee to work on the Kumaun Lake project mentioned above.
She defended her doctoral dissertation at IIT Roorkee in August 2008, after working in Dr. Routh’s lab for one year doing various analyses. The name of the thesis is ”Characterisation of organic matter in sediments of Kumaun Himalayas”. From 2012, she is once again back in Sweden, now working as a post-doc at the Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University.