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MONTANA  STATE  LIBRARY 

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BIOLOGICAL  INTEGRITY  OF  HUGHES  CREEK 

IN  THE 

BITTERROOT  RIVER  TMDL  PLANNING  AREA 

BASED  ON  THE  STRUCTURE  AND  COMPOSITION  OF 

THE  BENTHIC  ALGAE  COMMUNITY 


Prepared  for: 

State  of  Montana 

Department  of  Environmental  Quality 

P.O.  Box  200901 

Helena,  Montana    59620-0901 

Project  Officer:  Andy  Welch 
DEQ  Contract  No.  200012-10 


Prepared  by: 

Loren  L.  Bahls,  Ph.D. 

Hannaea 

1032  Twelfth  Avenue 

Helena,  Montana  59601 


January  31,  2004 


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HELENA.  MONTANA  59620 


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Summary 

On  the  Fourth  of  July,  2003,  periphyton  samples  were  collected  from  2  sites  on  Hughes 
Creek  in  the  Bitterroot  River  TMDL  planning  area  in  southwestern  Montana  for  the  purpose  of 
assessing  whether  this  stream  is  water-quality  limited  and  in  need  of  TMDLs.  The  samples  were 
collected  following  MDEQ  standard  operating  procedures,  processed  and  analyzed  using 
standard  methods  for  periphyton,  and  evaluated  following  modified  USEPA  rapid  bioassessment 
protocols  for  wadeable  streams. 

Diatom  metrics  at  both  sites  on  Hughes  Creek  indicated  excellent  biological 
integrity,  no  impairment,  and  full  support  of  aquatic  life  uses.  However,  values  for  the 
pollution  index  at  both  sites  approached  the  threshold  for  minor  impairment  and  indicate 
elevated  organic  loading.  This  organic  loading  may  be  natural  in  origin. 

A  large  amount  of  fine  sand  was  noted  in  the  sample  from  the  lower  site  on  Hughes 
Creek.  However,  values  for  the  sedimentation  index  were  well  below  the  threshold  for  minor 
impairment  in  a  mountain  stream.  Nevertheless,  both  sites  did  support  large  numbers  of 
Planothidium  lanceolatum,  a  diatom  that  is  adapted  to  living  on  grains  of  sand. 

The  diatom  and  non-diatom  algal  floras  of  Hughes  Creek  indicate  moderate  gradients  and 
current  velocities  with  little  disturbance,  and  cold,  alkaline,  and  highly  oxygenated  waters  with 
somewhat  elevated  levels  of  organic  and  inorganic  nutrients.  Nitrogen  is  probably  the  limiting 
nutrient  in  this  stream.  The  two  sites  supported  very  similar  floras,  which  indicates  very  similar 
ecological  conditions.  Diatom  species  richness,  diversity,  and  equitability  were  excellent.  No 
abnormal  diatom  cells  were  observed,  which  indicates  the  probable  absence  of  toxic  chemicals. 


Introduction 

This  report  evaluates  the  biological  integrity',  support  of  aquatic  life  uses,  and  probable 
causes  of  stress  or  impairment  to  aquatic  communities  in  Hughes  Creek  in  the  Bitterroot  River 
TMDL  planning  area  in  southwestern  Montana.    The  purpose  of  this  report  is  to  provide 

information  that  will  help  the  State  of  Montana  determine  whether  Hughes  Creek  is  water- 
quality  limited  and  in  need  of  TMDLs. 

The  federal  Clean  Water  Act  directs  states  to  develop  water  pollution  control  plans  (Total 
Maximum  Daily  Loads  or  TMDLs)  that  set  limits  on  pollution  loading  to  water-quality  limited 
waters.  Water-quality  limited  waters  are  lakes  and  stream  segments  that  do  not  meet  water- 
quality  standards,  that  is,  that  do  not  fUlly  support  their  beneficial  uses.  The  Clean  Water  Act 

and  USEPA  regulations  require  each  state  to  (1)  identify  waters  that  are  water-quality  limited, 
(2)  prioritize  and  target  waters  for  TMDLs,  and  (3)  develop  TMDL  plans  to  attain  and  maintain 
water-quality  standards  for  all  water-quality  limited  waters. 

Evaluation  of  aquatic  life  use  support  in  this  report  is  based  on  the  species  composition 
and  structure  of  periphyton  (benthic  algae,  phytobenthos)  communities  at  two  sites  on  Hughes 
Creek  that  were  sampled  on  July  4,  2003.  Periphyton  is  a  diverse  assortment  of  simple 
photosynthetic  organisms  called  algae  that  live  attached  to  or  in  close  proximity  of  the  stream 
bottom.  Some  algae  form  long  filaments  or  large  colonies  and  are  conspicuous  to  the  unaided 
eye.  But  most  algae,  including  the  ubiquitous  diatoms,  can  be  seen  and  identified  only  with  the 
aid  of  a  microscope.  The  periphyton  community  is  a  basic  biological  component  of  all  aquatic 
ecosystems.  Periph\1on  accounts  for  much  of  the  primary  production  and  biological  diversity  in 
Montana  streams  (Bahls  et  al.  1992).  Plafkin  et  al.  (1989)  and  Barbour  et  al.  (1999)  list  several 
advantages  of  using  periphyton  in  biological  assessments. 


'  Biological  integrity  is  defined  as  "the  ability  of  an  aquatic  ecosystem  to  support  and  maintain  a  balanced, 
integrated,  adaptive  community  of  organisms  having  a  species  composition,  diversity,  and  functional  organization 
comparable  to  that  of  namral  habitats  within  a  region"  (Karr  and  Dudley  1981). 


Project  Area  and  Sampling  Sites 

The  project  area  is  located  within  the  Montana  extension  of  the  Idaho  BathoHth 
Ecoregion  in  RavalH  County,  Montana.  This  ecoregion  is  mountainous,  deeply  dissected, 
partially  glaciated,  and  characteristically  underlain  by  granitic  rocks.  Soils  derived  from 
granitics  are  droughty  and  have  limited  fertility,  and  therefore  provide  only  limited  amounts  of 
nutrients  to  aquatic  systems  (McGrath  et  al.  2001).  Vegetation  in  the  project  area  is  mixed 
conifer  forest  at  higher  elevations  and  ponderosa  pine,  shrubs  and  grasses  at  lower  elevations 
(USDA  1976,  Woods  et  al.  1999).  The  main  land  uses  are  logging,  grazing,  recreation,  mining, 
and  wildlife  production.  Streams  in  this  ecoregion  are  likely  to  suffer  from  increased  loads  of 
fine  sediments  after  disturbance  by  humans,  hi  the  Idaho  portion  of  this  ecoregion,  logging  has 
caused  slope  instability  (especially  in  granitic  areas)  and  stream  sedimentation.  Placer  gold 
mining  has  heavily  affected  rivers  in  this  ecoregion  in  the  state  of  Idaho  (McGrath  et  al.  2001). 

Periphyton  samples  were  collected  at  two  sites  on  Hughes  Creek  (Table  1).  Elevation  at 
the  sampling  sites  is  about  5,700  feet.  Hughes  Creek  is  an  east-side  tributary  of  the  West  Fork  of 
the  Bitterroot  River  upstream  from  Painted  Rocks  Reservoir.    Hughes  Creek  and  the  West  Fork 
of  the  Bitterroot  River  are  headwater  tributaries  of  the  Bitterroot  River  in  USGS  hydrologic  unit 
17010205.  The  Bitterroot  River  is  a  tributary  of  the  Clark  Fork  River.    Hughes  Creek  is 
classified  B-1  in  the  Montana  Surface  Water  Quality  Standards. 

Methods 

Periphyton  samples  were  collected  following  standard  operating  procedures  of  the 
MDEQ  Planning,  Prevention,  and  Assistance  Division.  Using  appropriate  tools,  microalgae 
were  scraped,  brushed,  or  sucked  from  natural  substrates  in  proportion  to  the  importance  of  those 
substrates  at  each  study  site.  Macroalgae  were  picked  by  hand  in  proportion  to  their  abundance 
at  the  site.  All  collections  of  microalgae  and  macroalgae  were  pooled  into  a  common  container 
and  preserved  with  Lugol's  (IKI)  solution. 


The  samples  were  examined  to  estimate  the  relative  abundance  and  rank  by  biovolume  of 
diatoms  and  genera  of  soft  (non-diatom)  algae  according  to  the  method  described  in  Bahls 
(1993).  Soft  algae  were  identified  using  Smith  (1950),  Prescott  (1962,  1978),  John  et  al.  (2002), 
and  Wehr  and  Sheath  (2003).  These  books  also  served  as  references  on  the  ecology  of  the  soft 
algae,  along  with  Palmer  (1969,  1977). 

After  the  identification  of  soft  algae,  the  raw  periphyton  samples  were  cleaned  of  organic 
matter  using  sulfuric  acid,  potassium  dichromate,  and  hydrogen  peroxide.  Then  permanent 
diatom  slides  were  prepared  using  Naphrax,  a  high  refractive  index  mounting  medium,  following 
Standard  Methods  for  the  Examination  of  Water  and  Wastewater  (APHA  1 998).  At  least  300 
diatom  cells  (600  valves)  were  counted  at  random  and  identified  to  species.  The  following  were 
the  main  taxonomic  references  for  the  diatoms:  Krammer  and  Lange-Bertalot  1986,  1988, 
1991a,  1991b;  Lange-Bertalot  1993,  2001;  Krammer  1997a,  1997b,  2002;  Reichardt  1997,  1999. 
Diatom  naming  conventions  followed  those  adopted  by  the  Academy  of  Natural  Sciences  for 
USGS  NAWQA  samples  (Morales  and  Potapova  2000)  as  updated  in  2003  (Dr.  Eduardo 
Morales,  Academy  of  Natural  Sciences,  digital  communication).  Van  Dam  et  al.  (1994)  was  the 
main  ecological  reference  for  the  diatoms. 

The  diatom  proportional  counts  were  used  to  generate  an  array  of  diatom  association 
metrics.  A  metric  is  a  characteristic  of  the  biota  that  changes  in  some  predictable  way  with 
increased  human  influence  (Barbour  et  al.  1999).  Diatoms  are  particularly  usefial  in  generating 
metrics  because  there  is  a  wealth  of  information  available  in  the  literature  regarding  the  pollution 
tolerances  and  water  quality  preferences  of  common  diatom  species  (e.g.,  Lowe  1974,  Beaver 
1981,  Lange-Bertalot  1996,  Van  Dam  et  al.  1994). 

Values  for  selected  metrics  were  compared  to  biocriteria  (numeric  thresholds)  developed 
for  streams  in  the  Rocky  Mountain  ecoregions  of  Montana  (Table  2).  These  criteria  are  based  on 
metric  values  measured  in  least-impaired  reference  streams  (Bahls  et  al.  1992)  and  metric  values 
measured  in  streams  that  are  known  to  be  impaired  by  various  sources  and  causes  of  pollution 
(Bahls  1993).  The  biocriteria  in  Table  2  are  valid  only  for  samples  collected  during  the  summer 
field  season  (June  21 -September  21). 


The  criteria  in  Table  2  distinguish  among  four  levels  of  stress  or  impairment  and  three 
levels  of  aquatic  life  use  support:  (1)  no  impairment  or  only  minor  impairment  (full  support), 
(2)  moderate  impairment  (partial  support),  and  (3)  severe  impairment  (nonsupport).  These 
impairment  levels  correspond  to  excellent,  good,  fair,  and  poor  biological  integrity,  respectively. 
In  cold,  high-gradient  mountain  streams,  natural  stressors  will  often  mimic  the  effects  of  man- 
caused  impairment  on  some  metric  values. 

Quality  Assurance 

Several  steps  were  taken  to  assure  that  the  study  results  are  accurate  and  reproducible. 
Upon  receipt  of  the  samples,  station  and  sample  attribute  data  were  recorded  in  the  Montana 
Diatom  Database  and  the  samples  were  assigned  a  unique  number,  e.g.,  2953-01 .  The  first  part 
of  this  number  (2953)  designates  the  sampling  site  (Hughes  Creek  above  Thunder  Mountain 
Road)  and  the  second  part  (01)  designates  the  number  of  periphyton  samples  that  that  have  been 
collected  at  this  site  for  which  data  have  been  entered  into  the  Montana  Diatom  Database. 

Sample  observations  and  analyses  of  soft  (non-diatom)  algae  were  recorded  in  a  lab 
notebook  along  with  information  on  the  sample  label.  A  portion  of  the  raw  sample  was  used  to 
make  duplicate  diatom  slides.     The  slide  used  for  the  diatom  proportional  count  will  be 
deposited  in  the  Montana  Diatom  Collection  at  the  University  of  Montana  Herbarium  in 
Missoula.  The  duplicate  slide  will  be  retained  by  Hannaea  in  Helena.  Diatom  proportional 
counts  have  been  entered  into  the  Montana  Diatom  Database. 

Results  and  Discussion 

Results  are  presented  in  Tables  3,  4  and  5,  which  are  located  near  the  end  of  this  report 
following  the  references  section.  Appendix  A  contains  a  series  of  diatom  reports,  one  for  each 
sample.  Each  diatom  report  contains  an  alphabetical  list  of  diatom  species  in  that  sample  and 
their  percent  abundances,  and  values  for  65  different  diatom  metrics  and  ecological  attributes. 


Sample  Notes 

Hughes  Creek  below  first  FS  gate.    Clean  sample,  little  sediment  is  present. 

Hughes  Creek  above  Thunder  Mountain  Road.  Sediment  (-10  micron  diameter  fine 
sand)  is  extremely  heavy. 


Non-Diatom  Algae  (Table  3) 

The  two  sites  on  Hughes  Creek  supported  very  similar  algal  floras  consisting  of  green 
algae,  cyanobacteria,  diatoms,  and  a  chrysophyte.  The  lower  site  supported  three  more  genera  of 
non-diatom  algae  than  the  upper  site.  A  downstream  increase  in  the  number  of  non-diatom  algal 
genera  and  diatom  species  is  the  normal  pattern  in  mountain  streams. 

The  sample  collected  at  the  upper  site  on  Hughes  Creek  (below  first  gate  on  FS  parcel) 
was  dominated  by  a  filamentous  green  alga  (Ulothrix)  and  a  branched  cyanobacterium  with 
heterocysts  {Tolypothn.x)(Ta.b\e  3).    These  cold-water  algae  are  common  in  mountain  streams. 
Tolypothrix  is  capable  of  fixing  atmospheric  (molecular)  nitrogen,  which  is  an  advantage  in 
waters  that  are  poor  in  nitrogen.  Diatoms  were  abundant  at  this  site  and  ranked  3^''  in  biovolume. 
The  chrysophyte  Hydrurus  foetidus  ranked  4"^  and  was  rare. 

The  sample  collected  at  the  lower  site  on  Hughes  Creek  was  also  dominated  by 
Ulothrix.  The  cyanobacterium  Nostoc  ranked  2"*^  in  biovolume  here  and  was  a  co-dominant  with 
Ulothrix.  Like  Tolypothrix,  Nostoc  has  heterocysts,  is  a  nitrogen  fixer,  and  prefers  cold  waters. 
Diatoms  were  abundant  and  ranked  3"^  in  biovolume  at  the  lower  site.  Cells  of  the  chrysophyte 
Hydrurus  foetidus,  which  forms  slimy  mucilaginous  masses,  were  frequent  and  this  genus  ranked 
4'  in  biovolume  at  this  site.  Wehr  and  Sheath  (2003)  describe  Hydrurus  foetidus  as  follows: 

One  of  the  most  dramatic  examples  of  a  cold-water  stenotherm  is  the  mountain-stream 
dwelling  chrysophyte  Hydrurus  foetidus.    This  macroscopic,  brown,  gelatinous, 
unpleasant-smelling  alga  is  relatively  abundant  in  both  the  eastern  and  western  mountain 


streams  of  North  America.  The  gelatinous  envelope  in  which  the  cells  are  embedded  is 
exceedingly  tough  and  the  plant  frequently  covers  the  entire  surface  of  submerged  rocks 
and  has  caused  more  than  one  hiker  to  lose  his  or  her  footing  when  crossing  a  stream.  It 
normally  begins  to  disappear  when  water  temperatures  rise  much  above  1 0°C . . . Other 
requirements  for  this  species  apparently  include  low  pH  and  bright  sunlight. 

The  nitrogen-fixing  cyanophyte  Tolypothrix  was  frequent  at  the  lower  site  and  ranked  5"^, 
followed  by  the  branched  filamentous  green  alga  Stigeoclonium,  which  was  also  frequent. 
Stigeoclonium  is  tolerant  of  organic  pollution  and  its  presence  may  indicate  an  increase  in 
organic  loading  at  this  site. 

Diatoms  (Table  4) 

All  of  the  major  diatom  species  from  Hughes  Creek  are  included  in  pollution  tolerance 
classes  3  or  2,  and  are  either  sensitive  to  organic  pollution  or  only  somewhat  tolerant  of  organic 
pollution  (Table  4). 

Diatom  metrics  for  both  sites  on  Hughes  Creek  indicate  excellent  biological 
integrity,  no  impairment,  and  full  support  of  aquatic  life  uses  (Table  4).  However,  pollution 
index  values  at  both  sites  (2.53  and  2.54)  approached  the  threshold  for  minor  impairment  in  a 
mountain  stream  (2.50).  This  slight  organic  loading  may  be  natural  in  origin  and  due  to  an 
accumulation  of  terrestrial  plant  debris  and/or  algae.  Several  of  the  major  diatom  species  (e.g., 
Diatoma  mesodon,  Fragilaria  spp.,  Hannaea  arcus,  Staurosira  construens,  Synedra  spp.)  are 
free-living  and  indicate  a  history  of  stable  flows  at  these  sites  and  the  absence  of  recent  bottom- 
scouring  events.  These  diatoms  also  indicate  cold  waters. 

Although  sedimentation  index  values  did  not  exceed  the  threshold  for  minor  impairment 
at  either  site,  a  large  amount  of  fine  sand  was  noted  in  the  sample  collected  at  the  lower  site  (see 
sample  notes,  above).  This  site  also  had  the  larger  sedimentation  index  value  of  the  two  sites 
based  on  the  percentage  of  mofile  diatoms  that  were  counted.  In  addition  to  motile  diatoms, 
these  sites  supported  large  numbers  o{ Planothidium  lanceolatum,  a  diatom  species  that  is 
adapted  to  living  attached  to  grains  of  sand.  If  the  percentage  of  Planothidium  lanceolatum  at 


• 


these  sites  is  added  to  the  percentage  of  motile  diatoms,  sedimentation  index  values  would 
approach  but  still  not  exceed  the  threshold  for  minor  impairment  (Table  4). 

Both  sites  on  Hughes  Creek  supported  diatom  assemblages  with  excellent  species 
richness,  diversity,  and  equitability  for  a  mountain  stream.  The  relatively  small  percentage  of 
Achnanthidium  minutissimum  at  both  sites  indicates  a  stream  with  moderate  gradient  and  current 
velocity  and  little  physical  disturbance.  The  absence  of  teratological  (abnormal)  cells  indicates 
that  toxicity  from  heavy  metals  is  not  likely  to  be  a  problem  here. 

As  with  the  non-diatom  algae,  the  two  sites  on  Hughes  Creek  supported  very  similar 
diatom  assemblages.  The  percent  community  similarity  between  the  two  sites  was  60.35,  which 
indicates  very  similar  floras  and  ecological  conditions.  Adjacent  sites  on  the  same  stream 
without  intervening  tributaries  or  point  source  discharges  typically  share  60  percent  or  more  of 
their  diatom  assemblages  (Bahls  1993). 


Modal  Categories  of  Ecological  Attributes  (Table  5) 

Several  ecological  attributes  assigned  by  Stevenson  and  Van  Dam  et  al.  (1994)  were 
selected  from  the  diatom  reports  in  the  appendix  and  modal  categories  of  these  attributes  were 
extracted  to  characterize  water  quality  tendencies  in  Hughes  Creek  (Table  5).  Most  of  the 
diatoms  that  inhabit  Hughes  Creek  may  be  characterized  as  non-motile,  alkaliphilous,  and 
autotrophic,  while  tolerating  high  levels  of  organic  nitrogen  and  a  moderate  amount  of  organic 
loading.  They  prefer  meso-eutrophic  to  eutrophic,  fresh  waters,  and  exert  a  continuously  high 
demand  for  dissolved  oxygen.  These  categories  are  defined  by  Van  Dam  et  al.  (1994). 


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