Subterranean Ecosystems

Total Page:16

File Type:pdf, Size:1020Kb

Subterranean Ecosystems Reprintedfrom: ECOSYSTEMSOF THE WORLD 30 SUBTERRANEANECOSYSTEMS Editedby Prof. Dr. Horst Wilkens Zoologisches Institut und Zoologisches Museum der UniuersitcitHamburg, M artin-Luther- Kin g-P latz 3, 20146 Hamburg, Germany Prof. David C. Culver The American UniuersiQ, 4400 MassachusettsAuenue, Washington,DC 200I 6-8002, USA Dr. William F. Humphreys WesternAustralian Mus eum, Francis Street, Perth, WesternAustralia 6000, Australia 2000 ELSEVIER Amsterdam- Lausanne- New York- Oxford - Shannon- Singapore- Tokyo Chapter0 BACKGROUNDAND GLOSSARY W.F.HUMPHREYS INTRODUCTION within biospeleology,and the issuewill not be pursued here at length. As with other specialized subjects, a plethora of Trogiobiteswere long consideredto be phylogenetic terminology and definitions has come to surround, or distributional relicts driven into caves by climatic sometimesto obscure,the discipline of biospeleology change,especiaily in the Pleistocenerefugium model. (speleobiology,stygobiology, . .), terms sometimesso Recently, cave colonization has been viewed as an subtly different - even synonymous as to confound active process - the invasion of a vacant habitat. even researcherswithin the discipline (for a fuller Notwithstanding,the undergroundrealm does harbour treatmentsee, for instance,Camacho, 1992). many distributionaland phyletic relicts. The terminology coverssix main themes: Anchialine waters (inland groundwaterwith current ( I ) How a speciescame to be underground. marine connections)harbour a distinct (Sket, 1996) (2) The degree of dependenceof a specieson the and, in some areas! a predictable fauna (Yager and undergroundrealm. Humphreys,1996). (3) Whether a speciesshows adaptations to the under- Stygofaunawith marine ancestryare consideredto ground realm. colonize the shore line and to becomeisolated inland (4) Whether a species inhabits subterraneanvoids by marine regressionfollowing a period of manne filled r,vithwater or with air, and which part(s) of transgression(Stock, 1977; Boutin and Coineau,1990; each it inhabits. Notenboom,l99l ; Holsinger,1994). (5) The delimitation of the various hypogean sub- systems. The degreeof dependenceof a specieson the (6) The amountand origin of the energysource for the underground realm ecosyslem. As a backgroundto this volume,the main themesre- Organisms have many pathways of interaction with curring in biospeleologyare introduced below, followed subterraneanspaces (Gibert et al., 1994); some are by a Glossary. only found underground,while others move in and The subjectof cavesis well introducedby Gillieson out ol the hypogean realm. More than twenty spe- cial nomenclature schemes have proposed (1991), while the literature pertaining to karst hy- been to describethese relationships,based on morphological, drology, encountered especially in the context of behavioural,and ecological adaptationsof animals to stygofauna,is accessiblein Fordand Williams (1989). undergroundlife and on their presenceor absencein caves(troglofauna; see review in Camacho,1992). How a speciescame to be underground ln the Schiner-Racovitd system (Schiner, 1854; Racovitza,1907), cave-inhabiting animals are grouped This issueis coveredfrom dilferent stancesin several by their degreeofdependence on the caveenvironment: contributions to this volume (e.g. Chapter 21 by troglobitesare specieswhich do not existoutside caves; Holsinger,Chapter 22 by Humphreys,and Chapter3l troglophiles may live and reproduce underground as by Deharvengand Bedos) as the topic is all-pervasrve well as in the epigean domain; whlle n'ogloxenesdo 4 W.F.HUMPHREYS not normally feed underground, but may enter caves which togetherproduce the convergence,characteristic actively (regular trogloxene) or passively (acciden- of cave-adaptedanimals, that is termed troglomorphy. tal trogloxene).Additional criteria have subsequently These adaptations include morphological, ecologi- entered these purely ecological definitions, so that cal, physiologicaland behaviouralcharacteristics (Ta- they have become a variable mix of biological and ble0.1). morphologicalcriteria (Howarth, 1973:p. 142). The lack of detailed ecological information for Whether a speciesshows adaptations to the most cave-inhabitingspecies leads to ambiguity, and underground realm this is to some extent overcome by the concept of troglomorphy (Christiansen,1962), which permits Organisms have many pathways of interaction with classificationof the cave inhabitantsusing a iess am- the subterraneanrealm. While some are only found biguous morphologicaldefinition (troglomorphic/non- underground,others move in and out of the hypogean troglomorphic species)rather than the ecologicalone environmentas indicatedin the ecologicalclassification (troglobitic/troglophilic/trogloxenicspecies); but this of speciesby the terms troglo(stygo)bitic,troglophilic term is itself being infiltrated by behavioural and and trogloxenic. physiologicalattributes (Tabie 0.1). It is important to note that functionally these categoriesare more diffuse than is suggestedby their Table 0.1 ecological context. For example,while stygo(troglo)- Characteristicsof cave organismsrelative to surface organlsms xenesmay occur undergroundonly accidentally,they troglomorphies I may influencehappenings in the hypogeanrealm, for example,functioning either as predatorsor prey (e.g. Morphological Gibert et al. 1994: p. l1), as well as constituting Specializationof sensoryorgans (chemo-, hygro- thermo- and a subset of the allochthonousinputs from epigean baro-receptors) sources. Elongationo1' appendages In consideringtroglomorphic correlates (e.g. reduced Reductionof eyes,pigments and rvings eyes,pigment, wings etc.) it is necessaryto distinguish Cuticle thinning (in terrestrralarthropods) whether the traits are different from close epigean (in Foot modification Collernbolaand planthoppers) ancestors(apomorphic) or simply characteristicsof the Scalereduction (in fish) group or lineage(.plesiomorphic). E co I ogic al and l:ehoo io tu'uI Slowing metabolisms Whether a speciesinhabits subterranean voids Starvationresistance filled with water or with air, and which part(s) of each it inhabits Relaxctionand degencratronof circadranrhyhrns I n*,^.o.4 fe,",-.lit., While the Schiner Racovitrdsystem is often used for lncreasedegg volume both terrestrialand aquaticspecies! Gibert et al. (1994: Increasedlife span p. 13) have proposed stygo- (.sensulato) as the most Behauioural ecologicallydescriptive prefix for groundwaterfauna. Decreasedaggregation (in Collembola) Hence, troglofauna becomes restricted to terrestrial Reducedreaction to alarm substances(in fish) systems (see review in Camacho, 1992), while the Increasedsensitivity to vibratlon aquatic fauna is referred to generally as stvgofauna (Ginet Reducedintraspecific aggre:sion and Decou, 1977; Botosaneanu,1986; Gibert et al., 1994).There are complex parallel classifications I From Culver et al. (1995), after Chdstiansen(1992). in use for aquatic subterraneanorganisms (e.g. Boto- saneanu,1986: endpaper; Williams, 1984;Stanford and Many species found living underground display Ward, 1993). certain characteristictraits that are thought to be Gibert et al. (1994) followed the main Schiner adaptiveto undergroundlife. These include both the Racovitrdsystem, replacing the prefix "troglo-" by reduction or loss of characters(regressive evolution) "stygo-" (hence,stygoxene, stygophile, stygobite). ln and the enhancementof others(constructive evolution), porous aquifers,stygophiles are subdividedinto three BACKGROUNDAND GLOSSARY 5 categories:occasional hl,porheos, which comprises in some tropical areas(Cape Range, Australia), highly essentiallythe larvae, especially of aquatic insects, troglomorphic (and stygomorphic)species are found, of most of the benthos;amphibites, whose life cycle under certain conditions,to be leeding in sunlight at requires the use of both surface and groundwater the entrance to caves. However, even within caves, systems;and permanent hyporheos,which comprises the boundariesbetween zones are dynamic, shifting, a diverse assemblageof organismspresent in all life inter alia, accordingto the degreeof biogenic carbon stagesin the groundwateror in the benthic habitats dioxide production(dependent on periodicity of water an aerial epigeanstage is not requiredto completethe and energy inputs), the weather, the season and life cycle. major climatic events. The extent of the zones and Stygobitesare subdividedinto two classesofobliga- their vagility varies between caves according to the tory hypogeanforms: ubiqtdtousstygobites are widely relative sizes of entrancesand volume, and the size, presentin both karstic and alluvial groundwatersand shapeand arrangementof the chambers(see Racovita, are sometimes found very close to the surface. ln Chapter28, this volume). contrast,phreatobite species are stygobites that are restrictedto the deepgroundwater substrata of alluvial aquifers(Gibert et al., 1994). The amount and origin of the energy source for the ecosystem Delimitation of the various hypogean sub-systems In the absenceof light subterraneanecosystems have The hypogeanrealm used to be defined in terms of been consideredto be dependenton organic matter cavesand the degreeof darkness.The realizationthat fixed by photosynthesis and reaching the hypogean most caves had no openings to the surface (Curl, realms by various direct and indirect pathways. Routes 1966), and that troglobitic animals may inhabit the of entry are as diverseas logs being washedinto open immediatesubsurface spaces even in non-karsticareas
Recommended publications
  • Junior Cave Scientist Cave and Karst Program Activity Book Ages 5 – 12+
    National Park Service U.S. Department of the Interior Geologic Resources Division Junior Cave Scientist Cave and Karst Program Activity Book Ages 5 – 12+ Name: Age: Explore • Learn • Protect 1 Become a Junior Cave Scientist Caves and karst landscapes are found throughout the United States. These features are important as part of our Nation's geologic heritage. In this book, you will explore a fascinating and fragile underground world, learn about the values of caves and karst landscapes, and complete fun educational activities. Explore magnificent and beautiful caves. You will find an amazing underground world just beneath your feet! Learn about caves and karst systems and the work that cave scientists do. Protect our natural environments and the things that make caves and karst areas special. To earn your badge, complete at least activities. (Your Age) Activities in this book are marked with an age indicator. Look for the symbols below: Flashlight Lantern Helmet and Headlamp Ages 5 - 7 Ages 8 – 11 Ages 12 and Older Put a check next to your age indicator on each page that you complete. I received this book from: After completing the activities, there are two ways to receive your Junior Cave Scientist badge: • Return the completed book to a ranger at a participating park, or 2 • Visit go.nps.gov/jrcavesci What are Speleo-Fact: Mammoth Cave is the longest cave in world with over 405 miles (652 km) of connected passageways. Caves and Karst? Caves are naturally occurring voids, cavities, interconnected passageways, or alcoves in the earth. Caves preserve fossils, minerals, ecosystems, and records of past climates.
    [Show full text]
  • Hobbs, H.H., and D.C. Culver. 2009
    of the L"SA _~arional ~Ylogical Society, Inc. -~- J the ~ational Speleological Society, Inc. 13 Cave Avenue Ennrsville.Alabama 35810-4431, U.S.A. 256-852-1300 E-mail: [email protected] Web page: http://www.caves.org All rights reserved, including the right to reproduce this book or portions thereof in any fonn or by any means, mechanical or electronic, including photocopying, recording, or by any information storage or retrieval system without permission in writing from the publisher. All inquiries should be addressed to the National Speleological Society. Editors: Arthur N. Palmer and Margaret V. Palmer Graphics: M.Y. Palmer andA.N. Palmer Formatting and photograph preparation: A.N. Palmer Library of Congress Control Number: 2007943932 ISBN: 9781879961289 Printed in the U.S.A. ged; and they, their contents, and their biota deserve our protection. Try to leave no trace of your _-hDDiJ:tmcm~ are on private property, and land-owner relations can be delicate. For these reasons, specific ~ ~ ~ IJM inrhuinf in publications of the National Speleological Society. Caves can also pose a danger to those 'T who lack experience. Access to caves, and assistance in meeting the requirements for safe .~ lUI!~aticjeJ i1:r rarwrrring local chapters of the NSS. 15 Cave Biology An Overview of Cave Biology in the USA The transition zone of caves is a dynamic region of constant darkn (aphotic), but where the microclimate is noticeably still affected Horton H. Hobbs III and David C. Culver surface events. Fluctuations in temperature and humidity, decreasi diversity of species, and lower biomass reflect the influences of bo AVES have traditionally been considered exotic and rare habitats, epigean and hypogean environments.
    [Show full text]
  • Supplementary Material 16S Rrna Clone Library
    Kip et al. Biogeosciences (bg-2011-334) Supplementary Material 16S rRNA clone library To investigate the total bacterial community a clone library based on the 16S rRNA gene was performed of the pool Sphagnum mosses from Andorra peat, next to S. magellanicum some S. falcatulum was present in this pool and both these species were analysed. Both 16S clone libraries showed the presence of Alphaproteobacteria (17%), Verrucomicrobia (13%) and Gammaproteobacteria (2%) and since the distribution of bacterial genera among the two species was comparable an average was made. In total a 180 clones were sequenced and analyzed for the phylogenetic trees see Fig. A1 and A2 The 16S clone libraries showed a very diverse set of bacteria to be present inside or on Sphagnum mosses. Compared to other studies the microbial community in Sphagnum peat soils (Dedysh et al., 2006; Kulichevskaya et al., 2007a; Opelt and Berg, 2004) is comparable to the microbial community found here, inside and attached on the Sphagnum mosses of the Patagonian peatlands. Most of the clones showed sequence similarity to isolates or environmental samples originating from peat ecosystems, of which most of them originate from Siberian acidic peat bogs. This indicated that similar bacterial communities can be found in peatlands in the Northern and Southern hemisphere implying there is no big geographical difference in microbial diversity in peat bogs. Four out of five classes of Proteobacteria were present in the 16S rRNA clone library; Alfa-, Beta-, Gamma and Deltaproteobacteria. 42 % of the clones belonging to the Alphaproteobacteria showed a 96-97% to Acidophaera rubrifaciens, a member of the Rhodospirullales an acidophilic bacteriochlorophyll-producing bacterium isolated from acidic hotsprings and mine drainage (Hiraishi et al., 2000).
    [Show full text]
  • Glossary Animal Physiology
    Limnology 1 Weisse - WS99/00 Glossary Limnology 1 Biological Zonation of a lentic System: Most organisms can be classified on the basis of their typical habitat. Benthos: The community of plants and animals that live permanently in or on the sea bottom. Littoral (intertidal zone): The trophogenic zone along the shore till the compensation depth where NPP occurs. It is rich in species diversity and number - especially algae and higher plants. • Epilittoral: Sedentary organisms of the shoreline; e.g. macrophytes, diatoms, etc. • Profundal: Depths of 180m and deeper. Limnion: Temperature related zonation of the open water body of lentic systems; i.e. summer stratification due to solar radiation produces several trophic zones - see also ecological aspects - depth zones. • Epilimnion: The upper warm and illuminated surface layer of a lake; narrower than the trophogenic zone. • Metalimnion: The transitional zone between epi- and hypolimnion; i.e. the zone of the thermocline. • Hypolimnion: The cool and poorly illuminated bottom layer of a lake, below the thermocline. Nekton: Pelagic animals that are active swimmers; i.e. most of the adult fishes. Pelagial: The environment of the open water of a lake, away from the bottom, and not in close proximity to the shoreline. It is Lower in species number and diversity than the benthos. The pelagial of rivers exhibits a directed and continuos flux (spatial relocation = amountH2O/cross-surface area). Plankton: Passively drifting or weakly swimming organisms in fresh waters; i.e. microscopic plants, eggs, larval stages of the nekton and benthos (such as phyto-plankton, zoo-plankton). • Neuston: The epipelagic zone few centimeters below the waterline; i.e.
    [Show full text]
  • Troglofauna Survey at Koolyanobbing
    Troglofauna survey at Koolyanobbing Prepared for Portman Ltd by Bennelongia Pty Ltd November 2008 Report 2008/49 Troglofauna survey at Koolyanobbing Bennelongia Pty Ltd 64 Jersey Street Jolimont WA 6913 www.bennelongia.com.au ACN 124 110 167 November 2008 Report 2008/49 Bennelongia Pty Ltd Koolyanobbing troglofauna LIMITATION: This review has been prepared for use by Portman Ltd and its agents. Bennelongia accepts no liability or responsibility in respect of any use or reliance on the review by any third party. Bennelongia has not attempted to verify the accuracy and completeness of all information supplied by Portman. COPYRIGHT: The document has been prepared to the requirements of Portman. Copyright and any other Intellectual Property associated with the document belong to Bennelongia and may not be reproduced without written permission of Portman or Bennelongia. Client – Portman Ltd Report Version Prepared by Checked by Submitted to Client Method Date Draft report Vers. 1 Andrew Trotter Stuart Halse email 25.xi.08 Final report Andrew Trotter Stuart Halse email 12.xii.08 K:\Projects\B_PORT_01\Report\Koolyanobbing\BEC_Koolyanobbing_final_12.xii.08.docx ii Bennelongia Pty Ltd Koolyanobbing troglofauna Executive Summary This report provides the results of a troglofauna survey at Portman Ltd’s proposed mine sites in B and C Deposit (proposed B and C Pits) at Koolyanobbing, which is located approximately 50 km north of Southern Cross in the Yilgarn region of Western Australia. Portman is seeking environmental approval to mine B and C Deposits. The purpose of this survey was to document the troglofaunal community at the proposed mine sites and assess the potential impacts of the proposed mines on troglofauna.
    [Show full text]
  • Isolation of an Archaeon at the Prokaryote-Eukaryote Interface 3 4 Authors: 5 Hiroyuki Imachi1*, Masaru K
    bioRxiv preprint doi: https://doi.org/10.1101/726976; this version posted August 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Title: 2 Isolation of an archaeon at the prokaryote-eukaryote interface 3 4 Authors: 5 Hiroyuki Imachi1*, Masaru K. Nobu2*, Nozomi Nakahara1,3, Yuki Morono4, Miyuki 6 Ogawara1, Yoshihiro Takaki1, Yoshinori Takano5, Katsuyuki Uematsu6, Tetsuro Ikuta7, 7 Motoo Ito4, Yohei Matsui8, Masayuki Miyazaki1, Kazuyoshi Murata9, Yumi Saito1, Sanae 8 Sakai1, Chihong Song9, Eiji Tasumi1, Yuko Yamanaka1, Takashi Yamaguchi3, Yoichi 9 Kamagata2, Hideyuki Tamaki2 and Ken Takai1 10 11 *These authors contributed equally to this work. 12 13 Affiliations: 14 1Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), 15 Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan 16 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and 17 Technology (AIST), Tsukuba, Japan 18 3Department of Civil and Environmental Engineering, Nagaoka University of 19 Technology, Nagaoka, Japan 20 4Kochi Institute for Core Sample Research, X-star, JAMSTEC, Nankoku, Japan 21 5Biogeochemistry Program, Research Institute for Marine Resources Utilization, 22 JAMSTEC, Yokosuka, Japan 23 6Department of Marine and Earth Sciences, Marine Work Japan Ltd, Yokosuka, Japan 24 7Research Institute for Global Change, JAMSTEC, Yokosuka, Japan 25 8Research Institute for Marine Resources Utilization, JAMSTEC, Yokosuka, Japan 26 9National Institute for Physiological Sciences, Okazaki, Japan 27 28 Corresponding authors: 29 Hiroyuki Imachi, E-mail: [email protected] 30 Masaru K. Nobu, E-mail: [email protected] 31 32 33 1 bioRxiv preprint doi: https://doi.org/10.1101/726976; this version posted August 8, 2019.
    [Show full text]
  • Troglobitic Specimens Recorded
    655000 660000 665000 670000 675000 680000 685000 690000 695000 7450000 7445000 Deposit H Deposit I A3b (!*# (! Deposit B (! !((! Deposit G (! ^ 7440000 *# (! A2d Deposit C Legend (! (! Study Area Deposit D (! Deposit Deposit A Deposit F 7435000 Troglibitic specimens Mt Ella (! Anillini ‘sp. indet’. Deposit E (! Atelurinae ‘sp. indet.’ (! Cormocephalus 'CHI003'. A4 - -Pp (! Embioptera ‘sp. indet.’ 7430000 (! Hydrobiomorpha 'sp. indet.’ A4 - -Pp *# Meenoplidae ‘sp. indet.’ (! Nocticola ‘sp. indet.’ K A2d ^ Prethopalpus 'sp indet.' 0 2.5 5 !( Pseudodiploexochus ‘sp. nov.’ 7425000 Kilometres (! Trogiidae ‘sp. indet.’ Absolute Scale - 1:110,000 Figure: 4.3 Drawn: BG Project ID: 1459 Date: 12/2/2013 Troglobitic specimens recorded Coordinate System Unique Map ID: BG282 Name: GDA 1994 MGA Zone 50 Projection: Transverse Mercator Datum: GDA 1994 A3 Rio Tinto Greater West Angelas Subterranean Fauna Assessment This page has been left blank intentionally May 2013 34 Rio Tinto Greater West Angelas Subterranean Fauna Assessment 4.3 SUMMARY OF TROGLOFAUNA GROUPS RECORDED 4.3.1 Thysanura FAMILY NICOLETIIDAE Atelurinae ‘sp. Indet.’ A single specimen was collected from Deposit D in bore WAD 358. Pilbara thysanurans are poorly known and the taxonomy of Nicoletiidae is based on their DNA sequences rather than published species descriptions. Subterranean Atelurinae are well known throughout the Pilbara; however, nearly all of the species recognised to date appear to be range restricted. This specimen appears to be characteristic of the Pilbara nicoletiids. This species is a likely SRE. 4.3.2 Psocoptera FAMILY TROGIIDAE Trogiidae ‘sp. indet.’ A single specimen was collected from Deposit D in bore DDRC 006. Only identification to family level was possible.
    [Show full text]
  • Novel Phosphate-Solubilizing Bacteria Enhance Soil Phosphorus Cycling Following Ecological Restoration of Land Degraded by Mining
    The ISME Journal (2020) 14:1600–1613 https://doi.org/10.1038/s41396-020-0632-4 ARTICLE Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining 1 2 1 2 2 2 2 Jie-Liang Liang ● Jun Liu ● Pu Jia ● Tao-tao Yang ● Qing-wei Zeng ● Sheng-chang Zhang ● Bin Liao ● 1 1,2 Wen-sheng Shu ● Jin-tian Li Received: 22 October 2019 / Revised: 2 March 2020 / Accepted: 10 March 2020 / Published online: 23 March 2020 © The Author(s) 2020. This article is published with open access Abstract Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was 1234567890();,: 1234567890();,: predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling.
    [Show full text]
  • Mt Gibson Ranges - Iron Hill Deposits: Troglofauna Assessment
    Mt Gibson Ranges - Iron Hill Deposits: Troglofauna Assessment Prepared for: Mount Gibson Mining February 2016 Final Report Iron Hill Deposit Troglofauna Mount Gibson Mining Mt Gibson Ranges - Iron Hill Deposits: Troglofauna Assessment Bennelongia Pty Ltd 5 Bishop Street Jolimont WA 6913 P: (08) 9285 8722 F: (08) 9285 8811 E: [email protected] ACN: 124 110 167 Report Number: 244 Report Version Prepared by Reviewed by Submitted to Client Method Date Draft Andrew Trotter Stuart Halse email 10 August 2015 Stuart Halse Andrew Trotter Draft email 11 February 2016 Danilo Harms Danilo Harms Final Renee Young Stuart Halse email 26 February 2016 K:\Projects\B_MGIB_02\Survey Report_BEC_Iron Hill Deposit Troglofauna Survey Assessment_final16ii16 This document has been prepared to the requirements of the Client and is for the use by the Client, its agents, and Bennelongia Environmental Consultants. Copyright and any other Intellectual Property associated with the document belong to Bennelongia Environmental Consultants and may not be reproduced without written permission of the Client or Bennelongia. No liability or responsibility is accepted in respect of any use by a third party or for purposes other than for which the document was commissioned. Bennelongia has not attempted to verify the accuracy and completeness of information supplied by the Client. © Copyright 2014 Bennelongia Pty Ltd. vi Iron Hill Deposit Troglofauna Mount Gibson Mining EXECUTIVE SUMMARY Mt Gibson Mining Limited is proposing the development of the Iron Hill Deposits as a southerly extension to the existing Mt Gibson Ranges mine operations, located 77 km north-east of Wubin in the Murchison Province of the Yilgarn Craton.
    [Show full text]
  • Chapter 4: PROKARYOTIC DIVERSITY
    Chapter 4: PROKARYOTIC DIVERSITY 1. Prokaryote Habitats, Relationships & Biomes 2. Proteobacteria 3. Gram-negative and Phototropic Non-Proteobacteria 4. Gram-Positive Bacteria 5. Deeply Branching Bacteria 6. Archaea 1. Prokaryote Habitats, Relationships & Biomes Important Metabolic Terminology Oxygen tolerance/usage: aerobic – requires or can use oxygen (O2) anaerobic – does not require or cannot tolerate O2 Energy usage: phototroph – uses light as an energy source • all photosynthetic organisms chemotroph – acquires energy from organic or inorganic molecules • organotrophs – get energy from organic molecules • lithotrophs – get energy from inorganic molecules …more Important Terminology Carbon Source: autotroph – uses CO2 as a carbon source • e.g., photoautotrophs or chemoautotrophs heterotroph – requires an organic carbon source • e.g., chemoheterotroph – gets energy & carbon from organic molecules Oligotrophs require few nutrients, the opposite of eutrophs or copiotrophs Facultative vs Obligate (or Strict): facultative – “able to, but not requiring” • e.g., facultative anaerobes can survive w/ or w/o O2 obligate – “absolutely requires” • e.g., obligate anaerobes cannot survive in O2 Symbiotic Relationships Symbiotic relationships (close, direct interactions) between different organisms in nature are of several types: • e.g., humans have beneficial bacteria in their digestive tracts that also benefit from the food we eat (mutualism) Microbiomes All the microorganisms that inhabit a particular organism or environment (e.g., human or
    [Show full text]
  • 7.014 Lectures 16 &17: the Biosphere & Carbon and Energy Metabolism
    MIT Department of Biology 7.014 Introductory Biology, Spring 2005 7.014 Lectures 16 &17: The Biosphere & Carbon and Energy Metabolism Simplified Summary of Microbial Metabolism The metabolism of different types of organisms drives the biogeochemical cycles of the biosphere. Balanced oxidation and reduction reactions keep the system from “running down”. All living organisms can be ordered into two groups1, autotrophs and heterotrophs, according to what they use as their carbon source. Within these groups the metabolism of organisms can be further classified according to their source of energy and electrons. Autotrophs: Those organisms get their energy from light (photoautotrophs) or reduced inorganic compounds (chemoautotrophs), and their carbon from CO2 through one of the following processes: Photosynthesis (aerobic) — Light energy used to reduce CO2 to organic carbon using H2O as a source of electrons. O2 evolved from splitting H2O. (Plants, algae, cyanobacteria) Bacterial Photosynthesis (anaerobic) — Light energy used to reduce CO2 to organic carbon (same as photosynthesis). H2S is used as the electron donor instead of H2O. (e.g. purple sulfur bacteria) Chemosynthesis (aerobic) — Energy from the oxidation of inorganic molecules is used to reduce CO2 to organic carbon (bacteria only). -2 e.g. sulfur oxidizing bacteria H2S → S → SO4 + - • nitrifying bacteria NH4 → NO2 → NO3 iron oxidizing bacteria Fe+2 → Fe+3 methane oxidizing bacteria (methanotrophs) CH4 → CO2 Heterotrophs: These organisms get their energy and carbon from organic compounds (supplied by autotrophs through the food web) through one or more of the following processes: Aerobic Respiration (aerobic) ⎯ Oxidation of organic compounds to CO2 and H2O, yielding energy for biological work.
    [Show full text]
  • Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
    The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT.
    [Show full text]