Luis Comolli - Academia.edu (original) (raw)

Papers by Luis Comolli

A long-standing scientific interest in microbial ecology is the contrast responses to the oxidati... more A long-standing scientific interest in microbial ecology is the contrast responses to the oxidative stress between aerobic and anaerobic bacteria. To day, this has been almost impossible to address directly because of the absence of non-destructive chemical probe. Here we present a real-time comparative study of molecular changes in the aerotolerant Desulfovibrio vulgaris cells and in aerobic Caluobacter crescentis cells in atmospheric oxygen. Using non-invasive synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy, we successfully measured directly in real-time chemical and structural changes in cellular environments in D. vulgaris and in C. crescentis during their exposure to air. By comparing measurements, we were able to identify tight temporal changes in chemical bonds, functional groups, and chemical substructures in lipids, DNA, proteins, and polyglucose in D. vulgaris. Electron tomography provides direct visual images of the corresponding morphological changes.

Microscopy Today, 2005

Bacteria contain a wealth of mechanisms that organize their internal and external components into... more Bacteria contain a wealth of mechanisms that organize their internal and external components into a highly polar structure, frequently with distinctive shape, and constrain certain metabolic functions to particular parts of the cell. For example, cell division generally takes place at the middle of the cell, and a host of interacting proteins are involved in ensuring that the division site is positioned properly. Thus, in spite of the lingering perception among some scientists that these cells are simply bags of freely diffusing enzymes, there is much to be learned from ultrastructural studies. Light microscopy has given evidence of cytoskeletal components that presumably establish and maintain cell shape and participate in cell division.

Clays and Clay Minerals, Dec 1, 2015

Clay swelling, an important phenomenon in natural systems, can dramatically affect the properties... more Clay swelling, an important phenomenon in natural systems, can dramatically affect the properties of soils and sediments. Of particular interest in low-salinity, saturated systems are osmotic hydrates, forms of smectite in which the layer separation greatly exceeds the thickness of a single smectite layer due to the intercalation of water. In situ X-ray diffraction (XRD) studies have shown a strong link between ionic strength and average interlayer spacing in osmotic hydrates but also indicate the presence of structural disorder that has not been fully described. In the present study the structural state of expanded smectite in sodium chloride solutions was investigated by combining very low electron dose, highresolution cryogenic-transmission electron microscopy observations with XRD experiments. Wyoming smectite (SWy-2) was embedded in vitreous ice to evaluate clay structure in aqua. Lattice-fringe images showed that smectite equilibrated in aqueous, low-ionic-strength solutions, exists as individual smectite layers, osmotic hydrates composed of parallel layers, as well as disordered layer conformations. No evidence was found here for edge-to-sheet attractions, but significant variability in interlayer spacing was observed. Whether this variation could be explained by a dependence of the magnitude of long-range cohesive (van der Waals) forces on the number of layers in a smectite particle was investigated here. Calculations of the Hamaker constant for layer-layer interactions showed that van der Waals forces may span at least five layers plus the intervening water and confirmed that forces vary with layer number. Drying of the disordered osmotic hydrates induced re-aggregation of the smectite to form particles that exhibited coherent scattering domains. Clay disaggregation and restacking may be considered as an example of oriented attachment, with the unusual distinction that it may be cycled repeatedly by changing solution conditions.

Biological systems : open access, Aug 17, 2015

Applied Clay Science, Jun 1, 2020

The aluminosilicate layers of the swelling clay mineral montmorillonite, and the saturated pores ... more The aluminosilicate layers of the swelling clay mineral montmorillonite, and the saturated pores they delineate, control the mechanical properties and the transport of solutes in many natural and engineered environments. However, the structural basis of montmorillonite porosity remains poorly characterized due to the difficulty in visualizing hydrated samples in their native state. Here, we used cryogenic transmission electron microscopy (cryo-TEM) and cryo electron tomography (cryo-ET) to show that stacking defects within minimally altered, fully hydrated montmorillonite particles define multiscale porosity networks. Variations in layer lateral dimensions over tens to thousands of nanometers cause a range of topological and dynamic defects that generate pervasive curvature and introduce previously uncharacterized solute transport pathways. Observations of long-range rotational order between neighboring layers indicate that the layer-layer interactions that govern clay swelling involve three dimensional orienting forces that operate across nanoscale pores. These direct observations of the hierarchical structure of hydrated montmorillonite pore networks with nanoscale resolution reveal potentially general aspects of colloidal interactions in fluid-saturated clay minerals.

Molecular Microbiology, Apr 1, 2010

The bacterium Caulobacter crescentus has morphologically and functionally distinct cell poles tha... more The bacterium Caulobacter crescentus has morphologically and functionally distinct cell poles that undergo sequential changes during the cell cycle. We show that the PopZ oligomeric network forms polar ribosome exclusion zones that change function during cell cycle progression. The parS/ParB chromosomal centromere is tethered to PopZ at one pole prior to the initiation of DNA replication. During polar maturation, the PopZ-centromere tether is broken, and the PopZ zone at that pole then switches function to act as a recruitment factor for the ordered addition of multiple proteins that promote the transformation of the flagellated pole into a stalked pole. Stalked pole assembly, in turn, triggers the initiation of chromosome replication, which signals the formation of a new PopZ zone at the opposite cell pole, where it functions to anchor the newly duplicated centromere that has traversed the long axis of the cell. We propose that pole-specific control of PopZ function coordinates polar development and cell cycle progression by enabling independent assembly and tethering activities at the two cell poles.

Zenodo (CERN European Organization for Nuclear Research), Oct 18, 2019

These movies contain all data displayed in Figures of this manuscript

agriRxiv, 2023

Towards the end of 2021 and during the first two months of 2022 a heat wave hit the northeast of ... more Towards the end of 2021 and during the first two months of 2022 a heat wave hit the northeast of Argentina, part of southern Brazil, Paraguay, and Uruguay, after a prolonged drought. The effects were catastrophic for agriculture, biodiversity, and the local economy. Extreme climate events have become globally more common, and this fact has helped create a higher level of public awareness about global warming. All climate adaptation and mitigation strategies with a potential to have global impact are worth disseminating and discussing. For over two decades and a half we have committed heavily in the creation of the integrated agroforestry system we document here. The creation and continued leveraging of the system provide an example that it is possible to recover biodiversity and ecosystem services on lands previously eroded due to highly extractive exploitation without appropriate replenishment. Collaborations with public extension agencies have helped in capacity building and public outreach to show how an economic activity can be strengthen by the recovery of natural complexity. We believe that our project and similar ones should be one type of strategy in the toolkit for meeting the 2030 biodiversity targets, e.g., as discussed in the Conference of the Parties to the Convention on Biological Diversity (CBD COP 15) Global Biodiversity Framework. This Framework must try to give the world the toolkit to enable the 2050 vision of living in harmony with nature, achieving transformative change across our societies and putting nature on a path to recovery by 2030.

Cryo EM Image Modeling. (A) A slice from a tomographic reconstruction and partial surface renderi... more Cryo EM Image Modeling. (A) A slice from a tomographic reconstruction and partial surface rendering of the inner membrane obtained from the reconstruction. (B),(C), (D) Models of Inner and outer membranes for different stages of cell division. Color map: local curvature of the surface. Results Deflections due to FtsZ ring Dynamic Directed Growth Caulobacter cell wall

Microscopy and Microanalysis, Aug 1, 2013

Focused ion beam (FIB) milling as a means to prepare electron-transparent specimens for transmiss... more Focused ion beam (FIB) milling as a means to prepare electron-transparent specimens for transmission electron microscopy (TEM) is a well-established technique in materials science. Using a cryo-transfer stage, FIB micromachining can be extended to frozen specimens [1], opening the door to a range of exciting opportunities. We report on experiments using a new cryo-transfer system from Hummingbird Scientific installed on an FEI Quanta Dual-Beam FIB and discuss future prospects. This system allows for the transfer of a frozen specimen into and out of the FIB. The sample can be sectioned in the FIB to electron transparency, removed and then transferred to a cryo TEM stage for imaging in a TEM, all while maintaining the frozen state.

Of central interest in this study were microbial communities attached to sediment particles and i... more Of central interest in this study were microbial communities attached to sediment particles and in associated groundwater. Are the communities similar? What do the organisms look like and how do they associated with each other? Research was conducted on samples collected from the Department of Energy's (DOE) Rifle Integrated Field Research Challenge (IFRC) site in Rifle, Colorado, USA. This site served first as a test case for in situ bioremediation via biostimulation, and more recently as a location for studying the role of microbial communities in the carbon and other linked biogeochemical cycles. We addressed the question of the nature of planktonic to sediment-attached microbial communities using field and laboratory experimental studies with a range of methods that provide 2- and 3-dimensional topological information coupled to information about chemical speciation, organism type, and activity levels. The research leveraged data from metagenomics and proteomics analyses that obtained through parallel work at the Rifle site in the context of the IFRC. In this project we integrated characterization methods with extensive genomic sequence information and associated environmental data to better understand the processes that occur within groundwater and sediment-attached communities. Notable is the range of characterization methods, including scanning transmission x-ray microscopy (STXM),more » micro-EXAFS/XANES and microdiffraction and 2D and 3D cryo-electron tomographic analysis, and high-resolutino transmission electron microscope (HRTEM) analysis to characterize these natural microbial communities. A cryo-TEM work was unique because samples for electron microscopic characterization were cryo-plunged directly on site immediately after sampling. This step minimizes post-collection alterations, including cell damages and change of redox state. Among many achievements documented in publications listed at the end of this report, we highlight the following: 1) The development of a platform for routine correlative cryogenic microscopy and spectroscopy with samples prepared on-site. 2) The determination of which organisms dominate planktonic and biofilm communities in the subsurface. 3) Identification of microorganism-mineral associations and discovery of a novel mechanism that sustains activity of iron-reducing bacteria. 4) The detection of bacteria from the OP11-OD1-WWE3 (etc.) radiation and elucidation of their remarkable structural organization by cryog-TEM cryo-electron tomograhpy (cryo-ET). 5) Extensive analysis of biofilms and documentation of the association of cells and Se minerals. 6) The comparison of expressed c-type cytochromes between pure cultures of G. bemidjiensis and related field populations, provided insight into possible molecular mechanisms for U(VI) reduction in the aquifer. At least sixteen publications will result from this project (partial support), which provide both graduate student and post doctoral training.« less

Photosynthesis: Mechanisms and Effects, 1998

The interaction between cytochrome f (cyt f) and plastocyanin (Pc) has been proposed to involve t... more The interaction between cytochrome f (cyt f) and plastocyanin (Pc) has been proposed to involve the recognition of their structurally highly conserved positively (Lys cluster) and negatively charged patches (Glu/Asp clusters), respectively [1-3]. Biochemical, biophysical, and molecular dynamics studies with the isolated proteins support the conclusion of a binding with electrostatic characteristics, perhaps complemented with hydrophobic ones, for refs. see [5,10]. In order to test the hypothesis in vivolin situ mutants of C. reinhardtii were prepared with altered electrical charge for Lys 58, 65, 66 (large domain) and 188, 189 (small domain) and the single-flash-induced photooxidation of cyt f was studied in intact cells and in permeabilized-by-nebulization cells.The ionic strength (I) dependence of the reaction was also measured. In order to explore the electrostatic nature of the binding (first step in the reaction), to distinguish the effect of I on the overall reaction, we used an affinity chromatography approach. We find that the in vitro binding studies point to an electrostatic effect, probably involving the electrical determinants of a specific patch in cyt f. In nebulized cells, neutralization/inversion of charges in the Lys cluster generate a clear but moderate (10 fold) inhibition of cyt f photooxidation and the reaction depends on I in a complex way. In intact cells the maximal inhibition is not higher than 2-3 fold. It is concluded that in vivo, the Lys cluster has no mandatory role in the reaction with Pc, in agreement with [10].

This report, which focuses on innovation, is the third by The World in 2050 (TWI2050) initiative ... more This report, which focuses on innovation, is the third by The World in 2050 (TWI2050) initiative that was established by the International Institute for Applied Systems Analysis (IIASA) and other partners to provide scientific foundations for the UN’s 2030 Agenda for Sustainable Development. This report is based on the voluntary and collaborative effort of more than 60 authors and contributors from about 20 institutions globally, who met virtually to develop science-based strategies and pathways toward achieving the Sustainable Development Goals (SDGs).

doi: 10.3389/fmicb.2014.00367 Inter-species interconnections in acid mine drainage microbial comm... more doi: 10.3389/fmicb.2014.00367 Inter-species interconnections in acid mine drainage microbial communities

A long-standing scientific interest in microbial ecology is the contrast responses to the oxidati... more A long-standing scientific interest in microbial ecology is the contrast responses to the oxidative stress between aerobic and anaerobic bacteria. To day, this has been almost impossible to address directly because of the absence of non-destructive chemical probe. Here we present a real-time comparative study of molecular changes in the aerotolerant Desulfovibrio vulgaris cells and in aerobic Caluobacter crescentis cells in atmospheric oxygen. Using non-invasive synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy, we successfully measured directly in real-time chemical and structural changes in cellular environments in D. vulgaris and in C. crescentis during their exposure to air. By comparing measurements, we were able to identify tight temporal changes in chemical bonds, functional groups, and chemical substructures in lipids, DNA, proteins, and polyglucose in D. vulgaris. Electron tomography provides direct visual images of the corresponding morphological changes.

Microscopy Today, 2005

Bacteria contain a wealth of mechanisms that organize their internal and external components into... more Bacteria contain a wealth of mechanisms that organize their internal and external components into a highly polar structure, frequently with distinctive shape, and constrain certain metabolic functions to particular parts of the cell. For example, cell division generally takes place at the middle of the cell, and a host of interacting proteins are involved in ensuring that the division site is positioned properly. Thus, in spite of the lingering perception among some scientists that these cells are simply bags of freely diffusing enzymes, there is much to be learned from ultrastructural studies. Light microscopy has given evidence of cytoskeletal components that presumably establish and maintain cell shape and participate in cell division.

Clays and Clay Minerals, Dec 1, 2015

Clay swelling, an important phenomenon in natural systems, can dramatically affect the properties... more Clay swelling, an important phenomenon in natural systems, can dramatically affect the properties of soils and sediments. Of particular interest in low-salinity, saturated systems are osmotic hydrates, forms of smectite in which the layer separation greatly exceeds the thickness of a single smectite layer due to the intercalation of water. In situ X-ray diffraction (XRD) studies have shown a strong link between ionic strength and average interlayer spacing in osmotic hydrates but also indicate the presence of structural disorder that has not been fully described. In the present study the structural state of expanded smectite in sodium chloride solutions was investigated by combining very low electron dose, highresolution cryogenic-transmission electron microscopy observations with XRD experiments. Wyoming smectite (SWy-2) was embedded in vitreous ice to evaluate clay structure in aqua. Lattice-fringe images showed that smectite equilibrated in aqueous, low-ionic-strength solutions, exists as individual smectite layers, osmotic hydrates composed of parallel layers, as well as disordered layer conformations. No evidence was found here for edge-to-sheet attractions, but significant variability in interlayer spacing was observed. Whether this variation could be explained by a dependence of the magnitude of long-range cohesive (van der Waals) forces on the number of layers in a smectite particle was investigated here. Calculations of the Hamaker constant for layer-layer interactions showed that van der Waals forces may span at least five layers plus the intervening water and confirmed that forces vary with layer number. Drying of the disordered osmotic hydrates induced re-aggregation of the smectite to form particles that exhibited coherent scattering domains. Clay disaggregation and restacking may be considered as an example of oriented attachment, with the unusual distinction that it may be cycled repeatedly by changing solution conditions.

Biological systems : open access, Aug 17, 2015

Applied Clay Science, Jun 1, 2020

The aluminosilicate layers of the swelling clay mineral montmorillonite, and the saturated pores ... more The aluminosilicate layers of the swelling clay mineral montmorillonite, and the saturated pores they delineate, control the mechanical properties and the transport of solutes in many natural and engineered environments. However, the structural basis of montmorillonite porosity remains poorly characterized due to the difficulty in visualizing hydrated samples in their native state. Here, we used cryogenic transmission electron microscopy (cryo-TEM) and cryo electron tomography (cryo-ET) to show that stacking defects within minimally altered, fully hydrated montmorillonite particles define multiscale porosity networks. Variations in layer lateral dimensions over tens to thousands of nanometers cause a range of topological and dynamic defects that generate pervasive curvature and introduce previously uncharacterized solute transport pathways. Observations of long-range rotational order between neighboring layers indicate that the layer-layer interactions that govern clay swelling involve three dimensional orienting forces that operate across nanoscale pores. These direct observations of the hierarchical structure of hydrated montmorillonite pore networks with nanoscale resolution reveal potentially general aspects of colloidal interactions in fluid-saturated clay minerals.

Molecular Microbiology, Apr 1, 2010

The bacterium Caulobacter crescentus has morphologically and functionally distinct cell poles tha... more The bacterium Caulobacter crescentus has morphologically and functionally distinct cell poles that undergo sequential changes during the cell cycle. We show that the PopZ oligomeric network forms polar ribosome exclusion zones that change function during cell cycle progression. The parS/ParB chromosomal centromere is tethered to PopZ at one pole prior to the initiation of DNA replication. During polar maturation, the PopZ-centromere tether is broken, and the PopZ zone at that pole then switches function to act as a recruitment factor for the ordered addition of multiple proteins that promote the transformation of the flagellated pole into a stalked pole. Stalked pole assembly, in turn, triggers the initiation of chromosome replication, which signals the formation of a new PopZ zone at the opposite cell pole, where it functions to anchor the newly duplicated centromere that has traversed the long axis of the cell. We propose that pole-specific control of PopZ function coordinates polar development and cell cycle progression by enabling independent assembly and tethering activities at the two cell poles.

Zenodo (CERN European Organization for Nuclear Research), Oct 18, 2019

These movies contain all data displayed in Figures of this manuscript

agriRxiv, 2023

Towards the end of 2021 and during the first two months of 2022 a heat wave hit the northeast of ... more Towards the end of 2021 and during the first two months of 2022 a heat wave hit the northeast of Argentina, part of southern Brazil, Paraguay, and Uruguay, after a prolonged drought. The effects were catastrophic for agriculture, biodiversity, and the local economy. Extreme climate events have become globally more common, and this fact has helped create a higher level of public awareness about global warming. All climate adaptation and mitigation strategies with a potential to have global impact are worth disseminating and discussing. For over two decades and a half we have committed heavily in the creation of the integrated agroforestry system we document here. The creation and continued leveraging of the system provide an example that it is possible to recover biodiversity and ecosystem services on lands previously eroded due to highly extractive exploitation without appropriate replenishment. Collaborations with public extension agencies have helped in capacity building and public outreach to show how an economic activity can be strengthen by the recovery of natural complexity. We believe that our project and similar ones should be one type of strategy in the toolkit for meeting the 2030 biodiversity targets, e.g., as discussed in the Conference of the Parties to the Convention on Biological Diversity (CBD COP 15) Global Biodiversity Framework. This Framework must try to give the world the toolkit to enable the 2050 vision of living in harmony with nature, achieving transformative change across our societies and putting nature on a path to recovery by 2030.

Cryo EM Image Modeling. (A) A slice from a tomographic reconstruction and partial surface renderi... more Cryo EM Image Modeling. (A) A slice from a tomographic reconstruction and partial surface rendering of the inner membrane obtained from the reconstruction. (B),(C), (D) Models of Inner and outer membranes for different stages of cell division. Color map: local curvature of the surface. Results Deflections due to FtsZ ring Dynamic Directed Growth Caulobacter cell wall

Microscopy and Microanalysis, Aug 1, 2013

Focused ion beam (FIB) milling as a means to prepare electron-transparent specimens for transmiss... more Focused ion beam (FIB) milling as a means to prepare electron-transparent specimens for transmission electron microscopy (TEM) is a well-established technique in materials science. Using a cryo-transfer stage, FIB micromachining can be extended to frozen specimens [1], opening the door to a range of exciting opportunities. We report on experiments using a new cryo-transfer system from Hummingbird Scientific installed on an FEI Quanta Dual-Beam FIB and discuss future prospects. This system allows for the transfer of a frozen specimen into and out of the FIB. The sample can be sectioned in the FIB to electron transparency, removed and then transferred to a cryo TEM stage for imaging in a TEM, all while maintaining the frozen state.

Of central interest in this study were microbial communities attached to sediment particles and i... more Of central interest in this study were microbial communities attached to sediment particles and in associated groundwater. Are the communities similar? What do the organisms look like and how do they associated with each other? Research was conducted on samples collected from the Department of Energy's (DOE) Rifle Integrated Field Research Challenge (IFRC) site in Rifle, Colorado, USA. This site served first as a test case for in situ bioremediation via biostimulation, and more recently as a location for studying the role of microbial communities in the carbon and other linked biogeochemical cycles. We addressed the question of the nature of planktonic to sediment-attached microbial communities using field and laboratory experimental studies with a range of methods that provide 2- and 3-dimensional topological information coupled to information about chemical speciation, organism type, and activity levels. The research leveraged data from metagenomics and proteomics analyses that obtained through parallel work at the Rifle site in the context of the IFRC. In this project we integrated characterization methods with extensive genomic sequence information and associated environmental data to better understand the processes that occur within groundwater and sediment-attached communities. Notable is the range of characterization methods, including scanning transmission x-ray microscopy (STXM),more » micro-EXAFS/XANES and microdiffraction and 2D and 3D cryo-electron tomographic analysis, and high-resolutino transmission electron microscope (HRTEM) analysis to characterize these natural microbial communities. A cryo-TEM work was unique because samples for electron microscopic characterization were cryo-plunged directly on site immediately after sampling. This step minimizes post-collection alterations, including cell damages and change of redox state. Among many achievements documented in publications listed at the end of this report, we highlight the following: 1) The development of a platform for routine correlative cryogenic microscopy and spectroscopy with samples prepared on-site. 2) The determination of which organisms dominate planktonic and biofilm communities in the subsurface. 3) Identification of microorganism-mineral associations and discovery of a novel mechanism that sustains activity of iron-reducing bacteria. 4) The detection of bacteria from the OP11-OD1-WWE3 (etc.) radiation and elucidation of their remarkable structural organization by cryog-TEM cryo-electron tomograhpy (cryo-ET). 5) Extensive analysis of biofilms and documentation of the association of cells and Se minerals. 6) The comparison of expressed c-type cytochromes between pure cultures of G. bemidjiensis and related field populations, provided insight into possible molecular mechanisms for U(VI) reduction in the aquifer. At least sixteen publications will result from this project (partial support), which provide both graduate student and post doctoral training.« less

Photosynthesis: Mechanisms and Effects, 1998

The interaction between cytochrome f (cyt f) and plastocyanin (Pc) has been proposed to involve t... more The interaction between cytochrome f (cyt f) and plastocyanin (Pc) has been proposed to involve the recognition of their structurally highly conserved positively (Lys cluster) and negatively charged patches (Glu/Asp clusters), respectively [1-3]. Biochemical, biophysical, and molecular dynamics studies with the isolated proteins support the conclusion of a binding with electrostatic characteristics, perhaps complemented with hydrophobic ones, for refs. see [5,10]. In order to test the hypothesis in vivolin situ mutants of C. reinhardtii were prepared with altered electrical charge for Lys 58, 65, 66 (large domain) and 188, 189 (small domain) and the single-flash-induced photooxidation of cyt f was studied in intact cells and in permeabilized-by-nebulization cells.The ionic strength (I) dependence of the reaction was also measured. In order to explore the electrostatic nature of the binding (first step in the reaction), to distinguish the effect of I on the overall reaction, we used an affinity chromatography approach. We find that the in vitro binding studies point to an electrostatic effect, probably involving the electrical determinants of a specific patch in cyt f. In nebulized cells, neutralization/inversion of charges in the Lys cluster generate a clear but moderate (10 fold) inhibition of cyt f photooxidation and the reaction depends on I in a complex way. In intact cells the maximal inhibition is not higher than 2-3 fold. It is concluded that in vivo, the Lys cluster has no mandatory role in the reaction with Pc, in agreement with [10].

This report, which focuses on innovation, is the third by The World in 2050 (TWI2050) initiative ... more This report, which focuses on innovation, is the third by The World in 2050 (TWI2050) initiative that was established by the International Institute for Applied Systems Analysis (IIASA) and other partners to provide scientific foundations for the UN’s 2030 Agenda for Sustainable Development. This report is based on the voluntary and collaborative effort of more than 60 authors and contributors from about 20 institutions globally, who met virtually to develop science-based strategies and pathways toward achieving the Sustainable Development Goals (SDGs).

doi: 10.3389/fmicb.2014.00367 Inter-species interconnections in acid mine drainage microbial comm... more doi: 10.3389/fmicb.2014.00367 Inter-species interconnections in acid mine drainage microbial communities